Velvet-Teaching
Category
Bioinformatics
Program On
Teaching
Version
1.2.10
Author / Distributor
Description
"Sequence assembler for very short reads" More details are at Velvet
Running Program
The last version of this application is at /usr/local/apps/eb/Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1
To use this version, please load the module with
ml Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_Velvet
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Velvet.%j.out
#SBATCH --error=Velvet.%j.err
cd $SLURM_SUBMIT_DIR
ml Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1
velveth [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1
velveth --help
velveth - simple hashing program
Version 1.2.10
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Compilation settings:
CATEGORIES = 2
MAXKMERLENGTH = 100
OPENMP
Usage:
./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename1 [filename2 ...]} {...} [options]
directory : directory name for output files
hash_length : EITHER an odd integer (if even, it will be decremented) <= 100 (if above, will be reduced)
: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 100 (if above, will be reduced)
and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
filename : path to sequence file or - for standard input
File format options:
-fasta -fastq -raw -fasta.gz -fastq.gz -raw.gz -sam -bam -fmtAuto
(Note: -fmtAuto will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
File layout options for paired reads (only for fasta and fastq formats):
-interleaved : File contains paired reads interleaved in the one file (default)
-separate : Read 2 separate files for paired reads
Read type options:
-short -shortPaired
-short2 -shortPaired2
-long -longPaired
-reference
Options:
-strand_specific : for strand specific transcriptome sequencing data (default: off)
-reuse_Sequences : reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
-reuse_binary : reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
-noHash : simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
-create_binary : create binary CnyUnifiedSeq file (default: off)
Synopsis:
- Short single end reads:
velveth Assem 29 -short -fastq s_1_sequence.txt
- Paired-end short reads (remember to interleave paired reads):
velveth Assem 31 -shortPaired -fasta interleaved.fna
- Paired-end short reads (using separate files for the paired reads)
velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa
- Two channels and some long reads:
velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta
- Three channels:
velveth Assem 35 -shortPaired -fasta pe_lib1.fasta -shortPaired2 pe_lib2.fasta -short3 se_lib1.fa
Output:
directory/Roadmaps
directory/Sequences
[Both files are picked up by graph, so please leave them there]
Installation
Source code is obtained from Velvet
System
64-bit Linux