DOKK / manpages / debian 10 / velvet-long / velvetg_63_long.1.en
VELVETG_63_LONG(1) User Commands VELVETG_63_LONG(1)

velvetg_63_long - de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63, LONGSEQUENCES)

Usage: ./velvetg directory [options]

: working directory name

: removal of low coverage nodes AFTER tour bus or allow the system to infer it
(default: no removal)
: expected distance between two paired end reads (default: no read pairing)
: tracking of short read positions in assembly (default: no tracking)
: minimum contig length exported to contigs.fa file (default: hash length * 2)
: export assembly to AMOS file (default: no export)
: 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)

: expected distance between two paired-end reads in the respective short-read dataset (default: no read pairing)
: expected distance between two long paired-end reads (default: no read pairing)
: est. standard deviation of respective dataset (default: 10% of corresponding length)
[replace '*' by nothing, '2' or '_long' as necessary]
: scaffolding of contigs used paired end information (default: on)
: 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)

: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
: removal of high coverage nodes AFTER tour bus (default: no removal)
: minimum coverage required for confident regions of contigs (default: 1)
: minimum number of long reads required to merge contigs (default: 2)
: export unused reads in UnusedReads.fa file (default: no)
: export a summary of contig alignment to the reference sequences (default: no)
: export the long nodes which were eliminated by the coverage filters (default: no)
: remove all the intermediary files which are useless for recalculation (default : no)
: remove all the intermediary files (no recalculation possible) (default: no)
: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
: for mate-pair libraries, indicate that the library might be contaminated with paired-end reads (default no)
: preserve sequences with long reads in them (default no)

: fasta file of contigs longer than twice hash length
: stats file (tab-spaced) useful for determining appropriate coverage cutoff
: special formatted file with all the information on the final graph
: (if requested) AMOS compatible assembly file
July 2018 velvetg_63_long 1.2.10+dfsg1