Difference between revisions of "Velvet"

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m (Text replace - "De Bruijn graph" to "Sequence assembly (de-novo assembly)")
 
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{{Bioinformatics application
 
{{Bioinformatics application
 
|sw summary=Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD
 
|sw summary=Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD
−
|bio domain=De-novo assembly,
+
|bio domain=Sequence assembly (de novo assembly),
−
|bio method=Assembly, De Bruijn graph,
+
|bio method=Sequence assembly, Sequence assembly (de-novo assembly),
 
|bio tech=Illumina, 454, ABI SOLiD,
 
|bio tech=Illumina, 454, ABI SOLiD,
 
|created by=Zerbino, D; Birney, E
 
|created by=Zerbino, D; Birney, E
 
|created at=European Bioinformatics Institute
 
|created at=European Bioinformatics Institute
−
|input format=FASTA, FASTQ, ELAND, GERALD, fasta.gz, fastq.gz
+
|maintained=Yes
 +
|input format=FASTA, FASTQ, Fasta.gz, Fastq.gz, SAM, BAM, Eland, Gerald
 
|licence=GPL
 
|licence=GPL
 
}}
 
}}
−
Needs about 20-25X coverage and paired reads.
+
== Key features==
  
−
Colorspace aware but require SOLiD™ System de Novo Accessory Tools to process SOLiD reads before assembly. Also needs to compile separate colorspace aware binary.
+
* de Bruijn graphs based assembly algorithm
 +
* Handles paired-end reads, both short and long
 +
* Can combine 454 and Illumina data
 +
* Supports multi-threaded assembly (> v1.1)
  
  
Line 17: Line 21:
 
== velveth ==
 
== velveth ==
 
<pre>
 
<pre>
−
./velveth directory hash_length {[-file_format][-read_type] filename} [options]
+
velveth - simple hashing program
 +
Version 1.2.07
  
−
  directory       : directory name for output files
+
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
−
hash_length     : odd integer (if even, it will be decremented) <= 131
+
This is free software; see the source for copying conditions. There is NO
−
                    (if above, will be reduced)
+
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
−
filename         : path to sequence file or - for standard input
+
 
 +
Compilation settings:
 +
CATEGORIES = 3
 +
MAXKMERLENGTH = 149
 +
LONGSEQUENCES
 +
 
 +
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) <= 149 (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 <= 149 (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:
 
File format options:
−
-fasta | -fastq | -fasta.gz | -fastq.gz | -eland | -gerald
+
-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:
 
Read type options:
−
-short | -shortPaired | -short2 | -shortPaired2 | -long | -longPaired
+
-short -shortPaired
 +
-short2 -shortPaired2
 +
-short3 -shortPaired3
 +
-long -longPaired
 +
-reference
  
 
Options:
 
Options:
−
-strand_specific : for strand specific transcriptome sequencing data  
+
-strand_specific : for strand specific transcriptome sequencing data (default: off)
−
                    (default: off)
+
-reuse_Sequences : reuse 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:
 
Output:
−
directory/Roadmaps
+
directory/Roadmaps
−
directory/Sequences
+
directory/Sequences
 +
[Both files are picked up by graph, so please leave them there]
 +
</pre>
 +
 
 +
== velvetg ==
 +
<pre>
 +
velvetg - de Bruijn graph construction, error removal and repeat resolution
 +
Version 1.2.07
 +
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 = 3
 +
MAXKMERLENGTH = 149
 +
LONGSEQUENCES
 +
 
 +
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)
  
−
[Both files are picked up by velvetg, so please leave them there]
+
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>
 
</pre>
−
 
+
{{Links}}
−
== velveth ==
+
{{References}}
 +
{{Link box}}

Latest revision as of 16:13, 19 December 2015

Application data

Created by Zerbino, D; Birney, E
Biological application domain(s) Sequence assembly (de novo assembly)
Principal bioinformatics method(s) Sequence assembly, Sequence assembly (de-novo assembly)
Technology Illumina, 454, ABI SOLiD
Created at European Bioinformatics Institute
Maintained? Yes
Input format(s) FASTA, FASTQ, Fasta.gz, Fastq.gz, SAM, BAM, Eland, Gerald
Licence GPL

Summary: Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD

"Error: no local variable "counter" was set." is not a number.

Key features

  • de Bruijn graphs based assembly algorithm
  • Handles paired-end reads, both short and long
  • Can combine 454 and Illumina data
  • Supports multi-threaded assembly (> v1.1)


Usage

velveth

velveth - simple hashing program
Version 1.2.07

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 = 3
MAXKMERLENGTH = 149
LONGSEQUENCES

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) <= 149 (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 <= 149 (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
	-short3	-shortPaired3
	-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)
	-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]

velvetg

velvetg - de Bruijn graph construction, error removal and repeat resolution
Version 1.2.07
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 = 3
MAXKMERLENGTH = 149
LONGSEQUENCES

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

Links


References

  1. . 2008. Genome Research
  2. . 2009. PLoS One


To add a reference for Velvet, enter the PubMed ID in the field below and click 'Add'.

 


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