## FASTXTEND Fastxtend is an extension of FASTX-Toolkit package (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Fastxtend is based on the library developed in fastx toolkit, it is written is C and it extend the FASTX-Toolkit with four commands line tools for Short-Reads FASTA/FASTQ files preprocessing: - fastx_clean allows cleaning (adapters, N, quality) of the reads in fastq files. - fastx_duplicatedReads estimates the duplicates rate of reads (single or pair reads). It computes a rapid and accurate estimation of the duplicates rate of an initial read set using a sample of this read set. - fastx_mergepairs perform the merging of the paired reads and give some statistics (merged size, percent of pairs merged). - fastx_stats Fastxtend is distributed open-source under CeCILL FREE SOFTWARE LICENSE. Check out http://www.cecill.info/ for more information about the contents of this license. Fastxtend home on the web is http://www.genoscope.cns.fr/fastxtend/ ## COMMAND LINE ARGUMENTS - All of the tools show usage information with -h - The option -Q is not documented in the usages it corresponds to the ASCII offset (generally -Q 33) and performs with all commands. #### fastx_clean $ fastx_clean -h usage: fastx_clean [-h] [-a ADAPTER_FILE] [-D] [-l N] [-n N] [-M N] [-m N] [-p N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE] Developped at Genoscope using the FASTX Toolkit 0.0.13.1 [-h] = This helpful help screen. [-a ADAPTER_FILE] = ADAPTER file in fasta format. [-j] = Keep the longest sequence before adaptater. [-l N] = Discard sequences shorter than N nucleotides. default is 10. [-q N] = Quality threshold - nucleotides with lower quality will be trimmed (from both ends of the sequence). default value is 2, use 0 to inactivate this trimming. [-n N] = Trim sequences after N unknown nucleotides. default is 0 = off. This cleaning is done on the trimmed (adapter + quality) sequence. [-c] = Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter). [-C] = Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter). [-k] = Report Adapter-Only sequences. [-v] = Verbose - report number of sequences. If [-o] is specified, report will be printed to STDOUT. If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR. [-z] = Compress output with GZIP. [-D] = DEBUG output. [-M N] = Require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don't clip it. [-m N] = Maximum number of mismatches allowed, default is 3 [-p N] = Allow one mismatch every N bases, default is 5 so one mismatch allow every 5 nucleotides [-r] = Reverse complement the input fastx file and clip. [-f] = Clip the input fastx file in forward, default is true. [-e] = Recursive alignment : iterate alignments between sequence and adapters until a match is found. [-i INFILE] = FASTA/Q input file. default is STDIN. [-o OUTFILE] = FASTA/Q output file. default is STDOUT. [-s STAT_FILE] = Tabular output file which contains trimming details for each input sequence. #### fastx_duplicatedReads $ fastx_duplicatedReads -h usage: fastx_duplicatedReads [-h] [-v] [-i INFILE] [-o OUTFILE] Developped at Genoscope using the FASTX Toolkit 0.0.13.1 [-h] = This helpful help screen. [-s SAMPLE] = FASTA/Q input file of a sample extract from INFILE [-i INFILE] = FASTA/Q input file. Default is STDIN. [-t SAMPLE2] = FASTA/Q input file of a sample extract from INFILE2 (Optional) [-j INFILE2] = FASTA/Q input file for Read 2 (Optional) [-c INT] = Trim sides of reads by a specified percentage (default: 0%) #### fastx_mergepairs $ fastx_mergepairs -h usage: fastx_mergepairs [-h] [-l N] [-m N] [-i N] [-s] [-M] [-a INFILE1] [-b INFILE2] [-o OUTFILE] Developped at Genoscope using the FASTX Toolkit 0.0.13.1 [-h] = This helpful help screen. [-l N] = Fragment size of read 2 used for detecting an overlap, default is 40 [-m N] = Maximal number of mismatches of the alignment of read 1 and subpart of read2, default is 4 [-i N] = Minimal identity percent of the alignment of read 1 and subpart of read2, default is 90 [-L N] = Minimal size of the alignment, default is 15 [-s] = Silent mode [-a INFILE1] = FASTA/Q input file [-b INFILE2] = FASTA/Q input file [-o OUTFILE] = FASTA/Q output file [-u OUTFILE1] = FASTA/Q output file of unpaired reads (e.g. merged reads). [-p OUTFILE1] = FASTA/Q output file of paired reads (e.g. non-merged reads). [-q OUTFILE1a] = FASTA/Q output file of read1 from paired reads (e.g. non-merged reads). [-r OUTFILE1b] = FASTA/Q output file of read2 from paired reads (e.g. non-merged reads). Choose between [-o] and [-u],[-p] and [-u],[-q],[-r] arguments. [-x FILE] = Print distribution of overlap size between read1 and read2 [-M] = Only print merged pairs, default is no. #### fastx_stats $ fastx_stats -h usage: fastx_stats [[-h] [-f INFILE] [-q]] [-h] = This helpful help screen. [-f INFILE] = FASTA/Q input file. default is STDIN. [-q] = Display quality values distribution. ## PRE-REQUISITES - A Linux based operating system. - Binaries are provided for the following platform : Linux x86_64 - g++ with gcc 4.1.2 or higher ## INSTALLATION 1. Clone this GitHub repository 2. Compile sources `make;` 3. Install binaries `make install` This will install the tools into ./bin ## More informations If you have questions about Fastxtend, you may ask them to sengelen [at] genoscope [.] cns [.] fr and jmaury [at] genoscope [.] cns [.] fr . You may also create an issue to ask questions on github website: https://github.com/institut-de-genomique/fastxtend/issues. ## ACKNOWLEDGMENTS Stefan Engelen, Cyril Firmo and Jean-Marc Aury - Fastxtend's authors This work was financially supported by the Genoscope, Institut de Genomique, CEA and Agence Nationale de la Recherche (ANR), and France Génomique (ANR-10-INBS-09-08).