Velvet-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=Velvet.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=Velvet.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=Velvet.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1 | ml Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1 | ||
velveth --help | |||
velveth - simple hashing program | velveth - simple hashing program | ||
Version 1.2.10 | Version 1.2.10 |
Latest revision as of 13:10, 10 August 2018
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