.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
.TH VELVETG_LONG "1" "July 2014" "velvetg_long 1.2.10+dfsg1" "User Commands"
.SH NAME
velvetg_long \- de Bruijn graph construction, error removal and repeat resolution (LONGSEQUENCES)
.SH DESCRIPTION
Usage:
\&./velvetg directory [options]
.TP
directory
: working directory name
.SS "Standard options:"
.TP
\fB\-cov_cutoff\fR <floating\-point|auto>
: removal of low coverage nodes AFTER tour bus or allow the system to infer it
.IP
(default: no removal)
.TP
\fB\-ins_length\fR <integer>
: expected distance between two paired end reads (default: no read pairing)
.TP
\fB\-read_trkg\fR <yes|no>
: tracking of short read positions in assembly (default: no tracking)
.TP
\fB\-min_contig_lgth\fR <integer>
: minimum contig length exported to contigs.fa file (default: hash length * 2)
.TP
\fB\-amos_file\fR <yes|no>
: export assembly to AMOS file (default: no export)
.TP
\fB\-exp_cov\fR <floating point|auto>
: expected coverage of unique regions or allow the system to infer it
.IP
(default: no long or paired\-end read resolution)
.HP
\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
.IP
(default: no removal)
.SS "Advanced options:"
.TP
\fB\-ins_length\fR* <integer>
: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
.TP
\fB\-ins_length_long\fR <integer>
: expected distance between two long paired\-end reads (default: no read pairing)
.TP
\fB\-ins_length\fR*_sd <integer>
: est. standard deviation of respective dataset (default: 10% of corresponding length)
.IP
[replace '*' by nothing, '2' or '_long' as necessary]
.TP
\fB\-scaffolding\fR <yes|no>
: scaffolding of contigs used paired end information (default: on)
.TP
\fB\-max_branch_length\fR <integer>
: maximum length in base pair of bubble (default: 100)
.HP
\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
.TP
\fB\-max_gap_count\fR <integer>
: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
.TP
\fB\-min_pair_count\fR <integer>
: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
.TP
\fB\-max_coverage\fR <floating point>
: removal of high coverage nodes AFTER tour bus (default: no removal)
.TP
\fB\-coverage_mask\fR <int>
: minimum coverage required for confident regions of contigs (default: 1)
.TP
\fB\-long_mult_cutoff\fR <int>
: minimum number of long reads required to merge contigs (default: 2)
.TP
\fB\-unused_reads\fR <yes|no>
: export unused reads in UnusedReads.fa file (default: no)
.TP
\fB\-alignments\fR <yes|no>
: export a summary of contig alignment to the reference sequences (default: no)
.TP
\fB\-exportFiltered\fR <yes|no>
: export the long nodes which were eliminated by the coverage filters (default: no)
.TP
\fB\-clean\fR <yes|no>
: remove all the intermediary files which are useless for recalculation (default : no)
.TP
\fB\-very_clean\fR <yes|no>
: remove all the intermediary files (no recalculation possible) (default: no)
.TP
\fB\-paired_exp_fraction\fR <double>
: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
.TP
\fB\-shortMatePaired\fR* <yes|no>
: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
.TP
\fB\-conserveLong\fR <yes|no>
: preserve sequences with long reads in them (default no)
.SS "Output:"
.TP
directory/contigs.fa
: fasta file of contigs longer than twice hash length
.TP
directory/stats.txt
: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
.TP
directory/LastGraph
: special formatted file with all the information on the final graph
.TP
directory/velvet_asm.afg
: (if requested) AMOS compatible assembly file