NAME
velvetg - de Bruijn graph construction, error removal and repeat
resolution
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)
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 0.7.61
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)
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
velvetg - de Bruijn graph constructMay,2010or removal and repeat resVELVETG(1)