Velvet
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Application data |
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| Created by | Zerbino, D; Birney, E |
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| 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
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