Shtsai at 01:39, 5 April 2026

2026-04-05T01:39:56Z

← Older revision		Revision as of 21:39, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]

	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	1.2.10		1.2.10

	=== Author / Distributor ===		== Author / Distributor ==
	Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18:821-829		Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18:821-829

	=== Description ===		== Description ==
	Sequence assembler for very short reads. More information: http://www.ebi.ac.uk/~zerbino/velvet/		Sequence assembler for very short reads. More information: http://www.ebi.ac.uk/~zerbino/velvet/

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	velveth - simple hashing program		velveth - simple hashing program

	=== Running Program ===		== Running Program ==
	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

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	For transcriptomic assembly, Velvet is extended by Oases.		For transcriptomic assembly, Velvet is extended by Oases.

	=== Documentation ===		== Documentation ==
	<pre class="gcommand">		<pre class="gcommand">
	module load Velvet/1.2.10-GCC-11.2.0-mt-kmer_191		module load Velvet/1.2.10-GCC-11.2.0-mt-kmer_191
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	source code download from http://www.ebi.ac.uk/~zerbino/velvet/		source code download from http://www.ebi.ac.uk/~zerbino/velvet/
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	velvet is compiled in multi-thread (compiled with 'LONGSEQUENCES=1' 'MAXKMERLENGTH=191' 'CATEGORIES=2' 'OPENMP=1')		velvet is compiled in multi-thread (compiled with 'LONGSEQUENCES=1' 'MAXKMERLENGTH=191' 'CATEGORIES=2' 'OPENMP=1')

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea: Updated for version 1.2.10-GCC-11.2.0

2023-09-06T19:16:26Z

Updated for version 1.2.10-GCC-11.2.0

← Older revision		Revision as of 15:16, 6 September 2023
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	some long reads causes segment fault with high categories (e.g. CATEGORIES=99), we suggest using the fitting categories and kmer version for less memory.		some long reads causes segment fault with high categories (e.g. CATEGORIES=99), we suggest using the fitting categories and kmer version for less memory.

	*Version 1.2.10, installed in /apps/eb/Velvet/1.2.10-GCC-8.3.0-mt-kmer_191/		*Version 1.2.10, installed in /apps/eb/Velvet/1.2.10-GCC-11.2.0-mt-kmer_191/

	To use this version of Velvet, please first load the module with		To use this version of Velvet, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load Velvet/1.2.10-GCC-8.3.0-mt-kmer_191		module load Velvet/1.2.10-GCC-11.2.0-mt-kmer_191
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml Velvet/1.2.10-GCC-8.3.0-mt-kmer_191		ml Velvet/1.2.10-GCC-11.2.0-mt-kmer_191

	export OMP_THREAD_LIMIT=24		export OMP_THREAD_LIMIT=24
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	=== Documentation ===		=== Documentation ===
	<pre class="gcommand">		<pre class="gcommand">
	module load Velvet/1.2.10-GCC-8.3.0-mt-kmer_191		module load Velvet/1.2.10-GCC-11.2.0-mt-kmer_191
	~~velveth --help~~

	velveth - simple hashing program		velveth - simple hashing program
	Version 1.2.10		Version 1.2.10
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	<pre class="gcommand">		<pre class="gcommand">
	module load Velvet/1.2.10-GCC-8.3.0-mt-kmer_191		module load Velvet/1.2.10-GCC-11.2.0-mt-kmer_191
	velvetg --help		velvetg --help

Moses: /* Running Program */

2021-09-08T18:13:43Z

Running Program

← Older revision		Revision as of 14:13, 8 September 2021
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	</pre>		</pre>

	In above sample, 24 in OMP_THREAD_LIMIT and OMP_NUM_THREADS are the number of threads to use. ntasks number has to match "24" in OMP_THREAD_LIMIT and OMP_NUM_THREADS		In the above sample, 24 for OMP_THREAD_LIMIT and OMP_NUM_THREADS are the number of threads to use. --ntasks number has to match the number "24" in OMP_THREAD_LIMIT and OMP_NUM_THREADS.

	Example of submission to the queue:		Example of submission to the queue:

Moses at 18:05, 8 September 2021

2021-09-08T18:05:46Z

Show changes

Moses: Created page with "Category:Sapelo2oldCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.10 === Author..."

2021-09-08T17:45:03Z

Created page with "Category:Sapelo2old Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.10 === Author..."

New page

[[Category:Sapelo2old]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

1.2.10

=== Author / Distributor ===

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18:821-829

=== Description ===

Sequence assembler for very short reads. More information: http://www.ebi.ac.uk/~zerbino/velvet/

velvetg - de Bruijn graph construction, error removal and repeat resolution
velveth - simple hashing program

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

Note:
velvet is compiled in multi-thread (compiled with 'BIGASSEMBLY=1' 'LONGSEQUENCES=1' 'MAXKMERLENGTH=100' 'CATEGORIES=62' 'OPENMP=1' )

some long reads causes segment fault with high categories (e.g. CATEGORIES=99), we suggest using the fitting categories and kmer version for less memory.

*Version 1.2.10, installed in /usr/local/apps/eb/Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1

To use this version of Velvet, please first load the module with
<pre class="gscript">
module load Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1
</pre>

Example of a shell script velvet.sh to run on at the batch queue:

<pre class="gscript">
#PBS -S /bin/bash
#PBS -N j_velvet
#PBS -q batch
#PBS -l nodes=1:ppn=2:AMD
#PBS -l walltime=480:00:00
#PBS -l mem=100gb

cd $PBS_O_WORKDIR

module load Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1

export OMP_THREAD_LIMIT=2
export OMP_NUM_THREADS=2
time velveth myDirectory 21 -shortPaired data/test_reads.fa
time velvetg myDirectory
</pre>

In above sample, 2 in OMP_THREAD_LIMIT and OMP_NUM_THREADS are the number of threads to use. ppn number has to match "2" in OMP_THREAD_LIMIT and OMP_NUM_THREADS

Example of submission to the queue:
<pre class="gcommand">
qsub velvet.sh
</pre>

Velvet needs large memory to run.

For transcriptomic assembly, Velvet is extended by Oases.

=== Documentation ===
<pre class="gcommand">
module load 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 = 62
MAXKMERLENGTH = 100
OPENMP
LONGSEQUENCES
BIGASSEMBLY

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
...
-short61 -shortPaired61
-short62 -shortPaired62
-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]

</pre>

[[#top|Back to Top]]

<pre class="gcommand">
module load Velvet/1.2.10-foss-2016b-mt-kmer_100-Perl-5.24.1
velvetg --help
Usage:
./velvetg directory [options]

directory : working directory name

Standard options:
-cov_cutoff <floating-point|auto> : removal of low coverage nodes AFTER tour bus or allow the system to infer it
(default: no removal)
-ins_length <integer> : expected distance between two paired end reads (default: no read pairing)
-read_trkg <yes|no> : tracking of short read positions in assembly (default: no tracking)
-min_contig_lgth <integer> : minimum contig length exported to contigs.fa file (default: hash length * 2)
-amos_file <yes|no> : export assembly to AMOS file (default: no export)
-exp_cov <floating point|auto> : expected coverage of unique regions or allow the system to infer it
(default: no long or paired-end read resolution)
-long_cov_cutoff <floating-point>: removal of nodes with low long-read coverage AFTER tour bus
(default: no removal)

Advanced options:
-ins_length* <integer> : expected distance between two paired-end reads in the respective short-read dataset (default: no read pairing)
-ins_length_long <integer> : expected distance between two long paired-end reads (default: no read pairing)
-ins_length*_sd <integer> : est. standard deviation of respective dataset (default: 10% of corresponding length)
[replace '*' by nothing, '2' or '_long' as necessary]
-scaffolding <yes|no> : scaffolding of contigs used paired end information (default: on)
-max_branch_length <integer> : maximum length in base pair of bubble (default: 100)
-max_divergence <floating-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
-max_gap_count <integer> : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
-min_pair_count <integer> : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
-max_coverage <floating point> : removal of high coverage nodes AFTER tour bus (default: no removal)
-coverage_mask <int> : minimum coverage required for confident regions of contigs (default: 1)
-long_mult_cutoff <int> : minimum number of long reads required to merge contigs (default: 2)
-unused_reads <yes|no> : export unused reads in UnusedReads.fa file (default: no)
-alignments <yes|no> : export a summary of contig alignment to the reference sequences (default: no)
-exportFiltered <yes|no> : export the long nodes which were eliminated by the coverage filters (default: no)
-clean <yes|no> : remove all the intermediary files which are useless for recalculation (default : no)
-very_clean <yes|no> : remove all the intermediary files (no recalculation possible) (default: no)
-paired_exp_fraction <double> : remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
-shortMatePaired* <yes|no> : for mate-pair libraries, indicate that the library might be contaminated with paired-end reads (default no)
-conserveLong <yes|no> : preserve sequences with long reads in them (default no)

Output:
directory/contigs.fa : fasta file of contigs longer than twice hash length
directory/stats.txt : stats file (tab-spaced) useful for determining appropriate coverage cutoff
directory/LastGraph : special formatted file with all the information on the final graph
directory/velvet_asm.afg : (if requested) AMOS compatible assembly file
</pre>

[[#top|Back to Top]]

=== Installation ===

source code download from http://www.ebi.ac.uk/~zerbino/velvet/

velvet is compiled in multi-thread (compiled with 'BIGASSEMBLY=1' 'LONGSEQUENCES=1' 'MAXKMERLENGTH=99' 'CATEGORIES=62' 'OPENMP=1' )

=== System ===
64-bit Linux

Velvet-Sapelo2 - Revision history

Shtsai at 01:39, 5 April 2026

Chelsea: Updated for version 1.2.10-GCC-11.2.0

Moses: /* Running Program */

Moses at 18:05, 8 September 2021

Moses: Created page with "Category:Sapelo2oldCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.10 === Author..."