sondovac: A TeX repository from uribe-convers

Sondovač 1.2 Basic help

Sondovač (English pronunciation is "Sondovach". The word is a Czech neologism 
meaning something like "The Prober" or "The Probe Maker") is a script to 
create orthologous low-copy nuclear probes from transcriptome and genome skim 
data for target enrichment.


Script summary
================================================================================

Phylogenetics benefits from using a large number of putatively independent 
nuclear loci and their combination with other sources of information, such as 
the plastid and mitochondrial genome. Selecting such orthologous low-copy 
nuclear (LCN) loci is still a challenge for non-model organisms. In recently 
published phylogenies based on target enrichment of several hundred LCN genes, 
these loci were selected from transcriptomes, genomes, gene expression studies, 
the literature, or a combination of these sources. Automated bioinformatic 
pipelines for the selection of LCN genes are, however, largely absent. We 
created a user-friendly, automated and interactive script named Sondovač to 
design LCN loci by a comparison between transcriptome and genome skim data. 
The script is licensed under open-source license GPL v.3 allowing further 
modifications. It runs on major Linux distributions and Mac OS X. Strong 
bioinformatics skills and access to high-performance computer clusters are not 
required; Sondovač runs on a standard desktop computer equipped with modern CPU 
like Intel i5 or i7.


Pipeline - how the data are processed
================================================================================

A transcriptome assembly and paired-end genome skim raw data are combined to 
get hundreds of orthologous LCN loci. Enrichment of multi-copy loci is 
minimized by using unique transcripts only, which are obtained by comparing all 
transcripts and removing those sharing ≥90% sequence similarity using BLAT. 
Before matching the genome skim data against those unique transcripts, reads of 
plastid (and mitochondrial) origin are removed with Bowtie 2, SAMtools and 
bam2fastq utilizing reference sequences. Paired-end reads are subsequently 
combined with FLASH. These processed reads are matched against the unique 
transcripts sharing ≥85% sequence similarity with BLAT. Transcripts with >1000 
BLAT hits (indicating repetitive elements) and BLAT hits containing masked 
nucleotides are removed before de novo assembly of the BLAT hits to larger 
contigs with Geneious, using the medium sensitivity / fast setting. After 
assembly, only those contigs that comprise exons of a minimum bait length 
(usually ≥120 bp in case of probe design for phylogenies) and have a certain 
minimum total locus length (multiple of the bait length, should not be too 
short in order to obtain sufficient phylogenetically informative signal; we 
recommend at least ≥600 bp) are retained. To ensure that probes do not target 
multiple similar loci, any probe sequences sharing ≥90% sequence similarity are 
removed using cd-hit-est, followed by a second filtering step for contigs 
containing exons of a minimum bait length and totaling minimum loci length (see 
comments above). To ensure that plastid sequences are absent from the probes, 
the probe sequences are matched against the plastome reference sharing ≥90% 
sequence similarity with BLAT and the hits removed from the probe set. The 
workflow of Sondovač is summarized in Figure 1 of the PDF manual.

The steps of Sondovač are consecutively numbered to aid comprehension.

Sondovač has three parts: two script parts and an intermediate part using 
Geneious. The workflow is as follows:

A) sondovac_part_a.sh: Covers steps 1 to 6.
  1)   Removal of transcripts sharing ≥90% sequence similarity.
  2)   Removal of reads of plastid origin.
  3)   Removal of reads of mitochondrial origin (optional).
  4)   Combination of paired-end reads.
  5)   Matching of the unique transcripts and the filtered, combined genome 
       skim reads sharing ≥85% sequence similarity.
  6)   Filtering of BLAT output:
  6.1) Choice of transcript or genome skim sequences for further processing.
  6.2) Removal of transcripts with >1000 BLAT hits.
  6.3) Removal of transcript or genome skim BLAT hits [depending on the 
       selection in (6.1)] containing masked nucleotides.

Input files for sondovac_part_a.sh are FASTA transcriptome data, FASTQ 
paired-end genome skim reads and a plastome (and possibly also mitochondriome) 
reference. The input file for Geneious is the output of sondovac_part_a.sh.

B) Geneious: Covers step 7 (see below and PDF manual)
  7)  De novo assembly of the transcript or genome skim BLAT hits [depending 
      on the selection in (6.1)] to larger contigs. Note that you need a copy 
      of Geneious for this step.

The output files of Geneious are input files for sondovac_part_b.sh.

C) sondovac_part_b.sh: Covers steps 8 to 11.
  8)  Retention of those contigs that comprise exons ≥ bait length and have a 
      certain total locus length.
  9)  Removal of probe sequences sharing ≥90% sequence similarity.
  10) Retention of those contigs that comprise exons ≥ bait length and have a 
      certain total locus length.
  11) Removal of probe sequences sharing ≥90% sequence similarity with the 
      plastome reference.

The output file of sondovac_part_b.sh is the final list of probes, from which 
the user needs to remove the putative plastid sequences indicated in step 11 of 
the pipeline.


Software dependencies and installation
================================================================================

Requirements to run Sondovač
--------------------------------------------------------------------------------

Sondovač uses several scientific software packages (namely bam2fastq, BLAT, 
Bowtie2, CD-HIT, FASTX toolkit, FLASH, Geneious, htsjdk, libgtextutils, Picard, 
and SAMtools - see required versions and links below), and basic UNIX tools 
(see below). Sondovač will check if those programs are installed - available in 
the PATH (i.e. if the shell application can locate and launch respective 
binaries). If you have those packages installed (in current versions), ensure 
that their binaries are in PATH. This should not be a problem for basic tools 
available in any UNIX-based operating system, as basic installation usually 
contains all needed tools. If you lack some of the required tools, the script 
will notify you, and you will have to install them manually. If this is 
needed, check the documentation for your operating system.

If required programs are not installed, Sondovač will offer you 
installation. You can use precompiled binaries available together with the 
script (this is the recommended option) or (sometimes) from the web. 
In case you would like to compile required software 
yourself, the script will guide you through this process. This is 
recommended only for advanced users, as compilation might sometimes be very 
tricky. Users of Mac OS X can install those applications also using Homebrew 
(see http://brew.sh/). For compilation you need Apache Ant, GNU G++, GNU GCC, 
GIT, Java/OpenJDK, libpng developmental files, and zlib developmental files. 
Ensure you have those tools available - they should be readily available for 
any UNIX-based operating system.

The following UNIX tools are required to run Sondovač. They are usually readily 
available in UNIX systems (but see note for Mac OS X below), so there is 
usually no need to install them manually. The tools are awk, bc, bunzip2, cat, 
cp, curl or wget, cut, dirname, dos2unis, echo, egrep, cd, g++, gcc, grep, 
gunzip, join, less, lsb_release or python (for Linux), make, mkdir, paste, 
perl, pkg-config, pwd, sed, sort, tar, tr, uname, uniq, unzip, wc.

sondovac_part_a.sh requires (and will install) the following software packages:
* BLAT
* Bowtie2
* SAMtools
* bam2fastq (will be replaced by Picard in a future release)
* FLASH
* FASTX-toolkit

sondovac_part_b.sh requires (and will install) the following software packages:
* CD-HIT
* BLAT

For Mac OS X users, Homebrew (http://brew.sh/ and https://github.com/Homebrew/) 
will be installed by the script, and it will install (new software or newer 
versions) Apache Ant, BASH (the shell interpreter), GNU AWK, GNU coreutils, GNU 
GCC, git, GNU grep, GNU make, pkg-config, GNU sed, and wget. Mac OS X is 
missing some tools and for others (typically sed, grep or awk) contains 
outdated BSD versions. The script will guide the user through the process, and 
it is possible to safely and easily remove these tools afterwards if the user 
wishes to do so.

See the PDF manual for details about tools required by Sondovač and their 
manual installation. For most users it should be sufficient to be guided by 
the script to install needed tools automatically.

When Sondovač starts, a directory "bin" is created in the current working 
directory. Sondovač saves binaries of required software packages in this 
directory (if they are not available). The user can then add this directory 
to PATH, move or delete it afterwards. See the PDF manual for details.

Geneious
--------------------------------------------------------------------------------

Geneious is a DNA alignment, assembly, and analysis software and one of the 
most common software platforms used in genomics. It is utilized for de novo 
assembly in Sondovač. We plan to replace it by a free open-source command 
line tool in a future release of Sondovač. Visit http://www.geneious.com/ 
for download, purchase, installation and usage of Geneious. After the input 
data are processed (interactively or not) by sondovac_part_a.sh, the user must 
process its output manually by Geneious according to the instructions given 
below. The output of Geneious is then processed by sondovac_part_b.sh, which 
produces the final probe set. Geneious was tested with versions 6, 7 and 8.

Import the output file of part A of the script (sondovac_part_a.sh): 
go to menu File | Import | From File... This file is named as:
*_blat_unique_transcripts_versus_genome_skim_data-no_missing_fin.fsa

Select the file and go to menu Tools | Align / Assemble | De Novo Assemble.
In "Data" frame select "Assemble by 1st (...) Underscore".
In "Method" frame select Geneious Assembler (if you don't have other 
assemblers, this option might be missing) and "Medium Sensitivity / Fast" 
Sensitivity.

In "Results" frame check "Save assembly report", "Save list of unused reads", 
"Save in sub-folder", "Save contigs" (do not check "Maximum") and "Save 
consensus sequences". Do not trim. Otherwise keep defaults. Run it. Geneious 
may warn about possible hanging because of big file size. Do not use Geneious 
for other tasks during the assembly. Running Geneious may take a long time.

Select all resulting contigs (typically named "* Contig #") and export them 
(go to menu File | Export | Selected Documents...) as "Tab-separated table 
values (*.tsv)". Save the following columns (Hold Ctrl key to mark more 
fields): "# Sequences", "% Pairwise Identity", "Description", "Mean Coverage", 
"Name" and "Sequence Length". If this option would be inaccessible for you, 
export all columns.

Warning! Do not select and export "* Consensus Sequences", "* Unused Reads" or 
"* Assembly Report" - only the individual "* contig #" files.

Select items "Consensus Sequences" and "Unused Reads" and export them as one 
FASTA. Go to menu File | Export | Selected Documents... and choose FASTA file 
type.

Use the exported files from Geneious as input for part B of the script 
(sondovac_part_b.sh).


Command-line parameters to run Sondovač
================================================================================

General parameters:
  Shared by sondovac_part_a.sh as well as sondovac_part_b.sh.

-h, -v   Print help message and exit.
-u       Check for updates. If there is newer version of Sondovač available on
           https://github.com/V-Z/sondovac/releases/, download of the newer 
           version will be offered to the user.
-l       Display LICENSE for license information (this script is licensed under 
           GNU GPL v.3, other software under variable licenses). Exit viewing 
           by pressing the "Q" key.
-r       Display README (this file) for detailed usage instructions. Exit 
           viewing by pressing the "Q" key. More information is available in 
           the  PDF manual.
-p       Display INSTALL for detailed installation instructions. Exit viewing 
           by pressing the "Q" key. More information is available in the PDF 
           manual.
-e       Display detailed citation information and exit. See the PDF manual for 
           more information.
-o       Set name of output files. Output files will start with that name. Do 
           not use spaces or special characters - some software can not handle 
           them correctly. Default value (if the user does not provide another 
           name) is "output". See below for the list of produced output files.
-i       Running in interactive mode - the script will on-demand ask for the 
	   required input files, installation of missing software etc. This is 
	   the recommended default value (the script runs interactively without 
	   explicitly using option "-n").
-n       Running in non-interactive mode. The user must provide at least the 
	   required input files (see below). You can use only one of parameters 
	   "-i" or "-n" (not both of them). If script fails to find some of the
	   required software packages, it will exit. This is recommended for 
	   batch or repeated analysis, on remote servers and for more advanced 
	   users. The user must be sure that all required software is installed 
	   (see INSTALL and PDF manual for details).

Input files:
  Those parameters are required when running in non-interactive mode.
  The parameters are optional in default interactive mode.
  Please, use file names without spaces and without special characters.

-f FILE  Transcriptome input file in FASTA format.
         sondovac_part_a.sh
-c FILE  Plastome reference sequence input file in FASTA format.
         sondovac_part_a.sh, sondovac_part_b.sh
         Plastome reference sequences from taxa up to the same order of the 
           studied plant group are suitable. See Shannon C K. Straub, Matthew 
           Parks, Kevin Weitemier, Mark Fishbein, Richard C. Cronn and Aaron 
           Liston; American Journal of Botany (2012) 99(2): 349-364, 
           http://www.amjbot.org/content/99/2/349.short
-m FILE  Mitochondriome reference sequence input file in FASTA format (optional)
         sondovac_part_a.sh
         This step is optional, as plant mitochondrial genomes have largely 
           variable sizes and high rearrangement rates.
-t FILE  Paired-end genome skim input file in FASTQ format (first file).
         sondovac_part_a.sh
-q FILE  Paired-end genome skim input file in FASTQ format (second file).
         sondovac_part_a.sh
-x FILE  Input file in TSV format (output of Geneious assembly).
         sondovac_part_b.sh
-z FILE  Input file in FASTA format (output of Geneious assembly).
         sondovac_part_b.sh

Optional parameters:
  See chapter "Pipeline" for steps referred here.
  If those parameters are not provided, the default values are used, and it is 
  not possible to change them at a later point (not even in interactive mode).

-a ###   Maximum overlap length expected in approximately ≥90% of read pairs 
	   (parameter -M of FLASH, see its manual for details). FLASH can not 
	   combine paired-end reads that do not overlap by at least 10 bp 
	   (default minimum overlap length).
         Step 4 of Sondovač, sondovac_part_a.sh.
         DEFAULT: 65
         OPTIONS: Integer ranging from 10 to 300
-y ##    Sequence similarity between unique transcripts and the filtered, 
           combined genome skim reads (parameter -minIdentity of BLAT, see its 
           manual for details). Filtering for orthologs, using sequence 
           similarity as criterion.
         Step 5 of Sondovač, sondovac_part_a.sh.
         DEFAULT: 85 (highly recommended)
         OPTIONS: Integer ranging from 70 to 100
-g       Choice of transcript or genome skim sequences for further processing. 
           Depending on the phylogenetic depth that should be obtained, the 
           probe sequences need to be designed from either the transcript or 
           genome skim sequences, or it might not matter (if the taxa, from 
           which the transcriptome and genome skim data were generated, are 
           closely related).
         Step 6.1 of Sondovač, sondovac_part_a.sh.
         DEFAULT: no usage of -g (genome skim sequences)
         OPTIONS: usage of -g (transcript sequences)
-s ####  Number of BLAT hits per transcript when matching unique transcripts 
           and the filtered, combined genome skim reads. Transcripts with a 
           high number of BLAT hits, indicating repetitive elements, need to 
           be removed from the putative probe sequences.
	 Step 6.2 of Sondovač, sondovac_part_a.sh.
         DEFAULT: 1000
         OPTIONS: Integer ranging from 100 to 10000
-b ###   Minimum exon (bait) length. The minimum exon length should not fall 
           below the bait length in order to account for specific binding 
           between genomic libraries and baits during hybridization.
         Steps 8 and 10 of Sondovač, sondovac_part_b.sh.
         DEFAULT: 120 (preferred length for phylogeny).
         OPTIONS: 80, 100, 120
-k ###   Minimum total locus length. When running the script in interactive 
           mode, the user will be asked which value to use. A table summarizing 
           the total number of LCN loci, which will be the result of the probe 
           design for all minimum total locus lengths that the user can select 
           (600 bp, 720 bp, 840 bp, 960 bp, 1080 bp, 1200 bp), will be 
           displayed to facilitate this choice.
         Steps 8 and 10 of Sondovač, sondovac_part_b.sh.
         DEFAULT: 600
         OPTIONS: 600, 720, 840, 960, 1080, 1200
-d 0.##  Sequence similarity between probe sequences (parameter -c of 
           cd-hit-est, see its manual for details). Probes that target multiple 
           similar loci need to be removed.
         Step 9 of Sondovač, sondovac_part_b.sh.
         DEFAULT: 0.9 (highly recommended).
         OPTIONS: Decimal ranging from 0.85 to 0.95
-y ##    Sequence similarity between probe sequences and plastome reference 
           (parameter -minIdentity of BLAT, see its manual for details). Some 
           plastid reads might not have been removed in step2; they should be 
           removed by this step.
         Step 11 of Sondovač, sondovac_part_b.sh.
         DEFAULT: 90 (highly recommended)
         OPTIONS: Integer ranging from 70 to 100


Examples:

The basic and most simple usage (running in interactive mode):
./sondovac_part_a.sh -i

Specify some of the required input files, otherwise run interactively:
./sondovac_part_a.sh -i -f input.fa -t reads1.fastq -q reads2.fastq

Running in non-interactive, automated mode:
./sondovac_part_a.sh -n -f input.fa -c referencecp.fa -m referencemt.fa \
  -t reads1.fastq -q reads2.fastq

Modify parameter "-a", otherwise run interactively:
./sondovac_part_a.sh -i -a 300

Run in non-interactive mode (parameter "-n") - in such case the user must 
  specify all required input files (parameters "-f", "-c", "-m", "-t" and 
"-q"). 
  Moreover, parameter "-y" is modified:
./sondovac_part_a.sh -n -f input.fa -c referencecp.fa -m referencemt.fa \
  -t reads1.fastq -q reads2.fastq -y 90

Modifying parameter "-s". Note that the interactive mode -i is implicit and 
  does not need to be specified explicitly:
./sondovac_part_a.sh -s 950


Input and output files
================================================================================

All names of input files and paths to them must be without spaces and without 
special characters (some software have difficulties handling these).

Script sondovac_part_a.sh requires as input files:
1) Transcriptome input file in FASTA format. Note: For technical reasons, the 
   labels of FASTA sequences must be unique numbers (no other characters). 
   Sondovač will check the labels, and if they are not in an appropriate form, 
   a copy of this input file with correct labels will be created.
2) Plastome reference sequence input file in FASTA format.
3) Paired-end genome skim input file in FASTQ format (two files - forward and 
   reverse reads).
4) OPTIONAL: Mitochondriome reference sequence input file in FASTA format.
   This file is not required.

Script sondovac_part_a.sh creates the following files:
1)  *_renamed.fasta - If needed, copy of the transcriptome input file with the 
      changed labels of the FASTA sequences (unique numbers corresponding to 
      the line numbers in the  original file) will be created. File 
2)  *_old_and_new_names.tsv then contains two columns: 1) the original 
      sequence labels as in the user-provided transcriptome input file and 2) 
      new sequence labels. This might be useful to trace back certain 
      sequences/probes. 1)  *_blat_unique_transcripts.psl - Output of BLAT 
      (removal of transcripts sharing ≥90% sequence similarity).
3)  *_unique_transcripts.fasta - Unique transcripts in FASTA format.
4)  *_genome_skim_data_no_cp_reads* - Genome skim data without cpDNA reads.
5)  *_genome_skim_data_no_cp_no_mt_reads* - Genome skim data without mtDNA 
      reads - only if mitochondriome reference sequence was used.
6)  *_combined_reads_co_cp_no_mt_reads* - Combined paired-end genome skim reads.
7)  *_blat_unique_transcripts_versus_genome_skim_data.pslx - Output of BLAT 
      (matching of the unique transcripts and the filtered, combined genome 
      skim reads sharing ≥85% sequence similarity).
8)  *_blat_unique_transcripts_versus_genome_skim_data.fasta - Matching 
      sequences in FASTA.
9) *_blat_unique_transcripts_versus_genome_skim_data-no_missing_fin.fsa - 
      Final FASTA sequences for usage in Geneious.
Files 1-8 are not necessary for further processing by this pipeline, but may be 
useful for the user. The last file (9) is used as input file for Geneious in 
the next step. An asterisk (*) denotes the beginning of the output files' names 
specified by the user with parameter "-o". If the user does not select a custom 
name, default value ("output") will be used.

Geneious requires as input the last output file of sondovac_part_a.sh (file 9: 
*_blat_unique_transcripts_versus_genome_skim_data-no_missing_fin.fsa).

Output of Geneious are two exported files (see Geneious chapter):
1) Final assembled sequences exported as TSV.
2) Final assembled sequences exported as FASTA.

Script sondovac_part_b.sh requires as input files:
1) Plastome reference sequence input file in FASTA format.
2) Assembled sequences exported from Geneious as TSV.
3) Assembled sequences exported from Geneious as FASTA.

Script sondovac_part_b.sh creates the following files:
1) *_prelim_probe_seq.fasta - Preliminary probe sequences.
2) *_prelim_probe_seq_cluster_100.fasta - Unclustered exons and clustered exons 
     with 100% sequence identity.
3) *_prelim_probe_seq_cluster_90.clstr - Unclustered exons and clustered exons 
     with more than a certain sequence similarity (CLSTR file).
4) *_unique_prelim_probe_seq.fasta - Unclustered exons / exons with less than a 
     certain sequence similarity.
5) *_similarity_test.fasta - Exons that comprise exons ≥ bait length and have 
     a certain total locus length.
6) *_target_enrichment_probe_sequences.fasta - Probes in FASTA.
7) *_possible_cp_dna_genes_in_probe_set.pslx - In case of any BLAT hits, the 
     user might need to manually remove these plastid probe sequences from 
     *_target_enrichment_probe_sequences.fasta (the previous script outfile); 
     the remaining ones are the final probe sequences in FASTA.

An asterisk (*) denotes the beginning of the output files' names specified by 
the user with parameter "-o". If user does not select a custom name, default 
value ("output") will be used.

By default, output files are created in the same directory from which Sondovač 
was launched. Output files can be saved in a custom directory by specifying an 
output directory together with parameter "-o":

# Find current directory (e.g. /home/user):
pwd
# Launching Sondovač located in directory /home/user/sondovac and save output 
# to e.g. desktop (/home/user/Desktop):
./sondovac/sondovac_part_a.sh -o Desktop/MyFile
# Sondovač will save software (if needed) in "bin" directory located in 
# directory from which it was launched, see it:
ls bin/*
# Output files are in desired directory, see them e.g. by:
ls -lh Desktop/MyFile*


Sample data
================================================================================

Together with the script, we provide the ZIP archive (1.8 GB) that contains 
example input files for running the script: Oxalis genome skim data as well 
as the Ricinus cpDNA and mtDNA reference sequences. See 
https://github.com/V-Z/sondovac/wiki/Sample-data for download of sample data.

The package contains:

1) input2_Ricinus_communis_reference_plastid_genome.fsa - cpDNA reference 
   (parameter -c), GenBank reference number NC_016736.
2) input3_J12_Oxalis_obtusa_J12_genome_skim_data_R1.fastq - paired-end genome 
   skim data, file 1 (parameter -t).
3) input4_J12_Oxalis_obtusa_J12_genome_skim_data_R2.fastq - paired-end genome 
   skim data, file 2 (parameter -q).
4) input5_Ricinus_communis_reference_mitochondrial_genome.fasta - mtDNA 
   reference (parameter -m), GenBank reference number NC_015141.

The transcriptome input file is unpublished data from G. K.-S. Wong et al. As 
soon as the data are published, we will post them on GitHub. Data can now 
be found under
* http://www.onekp.com/
* http://www.onekp.com/samples/list.php
* http://www.onekp.com/samples/single.php?id=JHCN

The transcriptome FASTA file used for the probe design is named 
JHCN-SOAPdenovo-Trans-assembly.dnas.out and can be found under 
JHCN/Assembly/JHCN-SOAPdenovo-Trans-translated/.

Information on access to data download is given in Matasci N, 
Hung L-H, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, 
Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, 
dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, 
Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, 
DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom 
RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, 
Leebens-Mack J and Wong G K-S (2014) Data access for the 1,000 Plants (1KP) 
project. GigaScience 3:17, http://www.gigasciencejournal.com/content/3/1/17/


Record output of Sondovač
================================================================================

To record the whole output of Sondovač (regardless of used parameters), use 
utility "tee". This will produce a plain text output with everything printed to 
the screen. It can be useful for reference or exploration if something went 
wrong. Use it as follows:

./sondovac_part_a.sh | tee records.log

You can use any command line arguments, script will behave as usual. The 
plain text file "records.log" will then contain all its output.


License
================================================================================

The script is licensed under permissive open-source license allowing 
redistribution and modifications. Check file LICENSE for details and feel free 
to enhance the script.


Citation
================================================================================

When using Sondovač please cite:

Roswitha Schmickl, Aaron Liston, Vojtěch Zeisek, Kenneth Oberlander, Kevin
  Weitemier, Shannon C.K. Straub, Richard C. Cronn, Léanne L. Dreyer and Jan 
  Suda
Phylogenetic marker development for target enrichment from transcriptome and
  genome skim data: the pipeline and its application in southern African 
  Oxalis (Oxalidaceae)
Molecular Ecology Resources (2016) - early view available on-line
http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12487/abstract


Other questions not covered here and reporting problems
================================================================================

If you have a question or you encounter a problem, please see 
https://github.com/V-Z/sondovac/issues and feel free to ask any question 
and/or express any wish. The authors will do their best to help you.


Software references
================================================================================

bam2fastq:
* http://gsl.hudsonalpha.org/information/software/bam2fastq
BLAT:
* W. James Kent
  BLAT – the BLAST-like alignment tool
  Genome Research (2002) 12:656-664
  http://genome.cshlp.org/content/12/4/656.short
Bowtie2:
* Ben Langmead and Steven L. Salzberg
  Fast gapped-read alignment with Bowtie 2
  Nature Methods (2012) 9:357-359
  http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html
CD-HIT:
* Weizhong Li, Lukasz Jaroszewski and Adam Godzik
  Clustering of highly homologous sequences to reduce the size of large
    protein databases
  Bioinformatics (2001) 17:282-283.
  http://bioinformatics.oxfordjournals.org/content/17/3/282.short
* Weizhong Li, Lukasz Jaroszewski and Adam Godzik
  Tolerating some redundancy significantly speeds up clustering of large
    protein databases
  Bioinformatics (2002) 18:77-82
  http://bioinformatics.oxfordjournals.org/content/18/1/77.short
* Weizhong Li and Adam Godzik
  Cd-hit: a fast program for clustering and comparing large sets of
    protein or nucleotide sequences
  Bioinformatics (2006) 22:1658-1659
  http://bioinformatics.oxfordjournals.org/content/22/13/1658.short
* Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu and Weizhong Li
  CD-HIT: accelerated for clustering the next generation sequencing data
  Bioinformatics (2012) 28:3150-3152
  http://bioinformatics.oxfordjournals.org/content/28/23/3150.short
* Ying Huang, Beifang Niu, Ying Gao, Limin Fu and Weizhong Li
  CD-HIT Suite: a web server for clustering and comparing biological sequences
  Bioinformatics (2010) 26:680
  http://bioinformatics.oxfordjournals.org/content/26/5/680.short
* Beifang Niu, Limin Fu, Shulei Sun and Weizhong Li
  Artificial and natural duplicates in pyrosequencing reads of metagenomic data
  BMC Bioinformatics (2010) 11:187
  http://www.biomedcentral.com/1471-2105/11/187
* Weizhong Li, Limin Fu, Beifang Niu, Sitao Wu and John Wooley
  Ultrafast clustering algorithms for metagenomic sequence analysis
  Briefings in Bioinformatics (2012) 13(6):656-668
  http://bib.oxfordjournals.org/content/13/6/656.abstract
FASTX toolkit:
* A. Gordon and G. J. Hannon
  FASTX-Toolkit. FASTQ/A short-reads pre-processing tools
  2010
  http://hannonlab.cshl.edu/fastx_toolkit/
FLASH:
* Tanja Magoč and Steven L. Salzberg
  FLASH: fast length adjustment of short reads to improve genome assemblies
  Bioinformatics (2011) 27(21):2957-2963
  http://bioinformatics.oxfordjournals.org/content/27/21/2957.abstract
Geneious
* Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew 
    Cheung, Shane Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris 
    Duran, Tobias Thierer, Bruce Ashton, Peter Meintjes1, and Alexei Drummond
  Geneious Basic: An integrated and extendable desktop software platform for 
    the organization and analysis of sequence data
  Bioinformatics (2012) 28(12):1647-1649
  http://bioinformatics.oxfordjournals.org/content/28/12/1647
grab_syngleton_clusters.py
* Kevin Weitemier, Shannon C K Straub, Richard C Cronn, Mark Fishbein, Roswitha 
    E. Schmickl, Angela McDonnell, Aaron Liston
  Hyb-Seq: Combining target enrichment and genome skimming for plant 
    phylogenomics
  Applications in Plant Sciences (2014) 2(9):1-7
  http://www.bioone.org/doi/abs/10.3732/apps.1400042
Picard:
* http://broadinstitute.github.io/picard
SAMtools:
* Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer,
    Gabor Marth, Goncalo Abecasis, Richard Durbin and 1000 Genome Project
    Data Processing Subgroup
  The Sequence Alignment/Map format and SAMtools
  Bioinformatics (2009) 25(16): 2078-2079
  http://bioinformatics.oxfordjournals.org/content/25/16/2078.abstract
* Heng Li
  A statistical framework for SNP calling, mutation discovery, association
    mapping and population genetical parameter estimation from sequencing data
  Bioinformatics (2011) 27(21): 2987-2993
  http://bioinformatics.oxfordjournals.org/content/27/21/2987.abstract
* Heng Li
  Improving SNP discovery by base alignment quality
  Bioinformatics (2011) 27(8): 1157-1158.
  http://bioinformatics.oxfordjournals.org/content/27/8/1157.short
uribe-convers/sondovac
