VELVETG(1)
NAME
velvetg - de Bruijn graph construction, error removal and repeat resolution (colorspace version)
DESCRIPTION
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)
- Advanced options:
- -ins_length2 <integer>
: expected distance between two paired-end reads in the second 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: 10)
- -max_coverage <floating point>
: removal of high coverage nodes AFTER tour bus (default: no removal)
- -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)
- 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
- Version 1.0.02
COPYRIGHT
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 = 31
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)
- Advanced options:
- -ins_length2 <integer>
: expected distance between two paired-end reads in the second 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: 10)
- -max_coverage <floating point>
: removal of high coverage nodes AFTER tour bus (default: no removal)
- -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)
- 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