Virusfishing version 1.1 (201801)
Virusfishing is a virus screening pipeline for 1000 Insect Transcriptome Evolution (1KITE) project to search viruses, construct viral genomes and screen for the expressed virus genes and discover viral splicing patterns. Virusfishing also can be used in other next generation sequencing data.
Include 3 steps:
- Search: search virus sequences from assembly
- Assemble: do virus assembly based on reference
- Splicing: identify splicing pattern of assembly
Virusfishing version 1.1 201801
tar -zxvf Virusfishing.V1.1.tar.gz
Virusfishing.py: the wrapper script to run other Perl scripts to do the work you choose.
Search virus:
Virus_Search.pl: search viruses in assemblies
Virus_false_removal.pl: removal false positive according to the taxonomy
Assemble viral gnome:
Ref_Based_Genome_Assemble.pl: assemble viral genomes based on viral reference
fq2fa.pl: change fastq files into fasta files
Detect splicing junctions:
Splicing_Search.pl: find introns and exon-exon splice junctions from the clean alignments and give out summaries
Summarize:
Virus_Coverage.pl: obtain the best-hit related sequences, and calculate the coverage of assembled sequences and viral sequences from the blast results.
Alignmentout_Sum.pl: filter multiple alignment file (support sam, bam, soap or map type) and make a summary for it.
Classify:
Find_NCBItax_from_name.pl: obtain the NCBI classification
You need to install following programs and add the software directories to your $PATH:
export PATH=:$PATH:$softwaredir # for sh or bash users
setenv PATH .:$PATH:$softwaredir # for csh users
Blastall 2.2.26
ftp.ncbi.nih.gov/blast/executables/blast+/2.2.26
BWA 0.7.10
bio-bwa.sourceforge.net
Bowtie2 (bowtie2-2.1.0 or higher)
bowtie-bio.sourceforge.net/bowtie2
TopHat2 (tophat-2.0.7 or higher)
ccb.jhu.edu/software/tophat
SAMtools-0.1.19 (include vcfutils.pl & bcftools)
sourceforge.net/projects/samtools/files/samtools/0.1.19
RefTools
github.com/BGI-shenzhen/Reseqtools
Python version 3 or higher
www.python.org
You need to install following libraries directories to your $ LD_LIBRARY_PATH:
export LD_LIBRARY_PATH=.:$boostdir
Boost
www.boost.org/
PerlIO::gzip
search.cpan.org/~nwclark/PerlIO-gzip-0.19/gzip.pm
ParseFasta.pm & ParseFastq.pm (already in Virusfishing.V1.1/lib/)
ftp.ncbi.nih.gov/blast/db/FASTA/
Or NCBI viral gene annotation
ftp://ftp.ncbi.nih.gov/refseq/release/viral/
Or Your own virus database
ftp.ncbi.nih.gov/blast/db/FASTA/
If Nt database is too large for you, you can do the 2nd blastn in step 1 and step 2 online.
blast.ncbi.nlm.nih.gov/Blast.cgi
(gi_taxid_nucl.dmp.gz, names.dmp & nodes.dmp)
ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
#Note: Creat symbolic links for databases in /Virusfishing.V1.1/database,
so that you can use the default parameter in some steps.
"ln -s /dir/names.dmp /Virusfishing.V1.1/database/tax/names.dmp"
-
Virus search:
python Virusfishing.V1.1/Virusfishing.py search -
Viral genome assemble:
python Virusfishing.V1.1/Virusfishing.py assemble -
Splice junction detection using raw data:
python Virusfishing.V1.1/Virusfishing.py splicing -
Only create a shell script for summarizing the alignment file:
perl Virusfishing.V1.1/bin/Alignmentout_Stat.pl -in in.map -ref ref.fa -type map -
Virus search without a NT database:
Perl Virusfishing.V1.1/bin/Virus_Search.pl -i assemble.fa -v virus.db -outpre candidateviral
Then, use the candidate viral sequences to blastn against NT database online
Chengran Zhou; Guanliang Meng; Wenhui Song; Jinmin Ma
Email: zhouchengran at genomics dot cn
mengguanliang at genomics dot cn
songwenhui at genomics dot cn
majinmin at genomics dot cn
Zhou, C., Liu, S., Song, W., Luo, S., Meng, G., Yang, C., Yang, H., Ma, J., Wang, L., Gao, S. and Wang, J., 2018. Characterization of viral RNA splicing using whole-transcriptome datasets from host species. Scientific reports, 8(1), p.3273. DOI: 10.1038/s41598-018-21190-7
Version 1.1 201801