velvetg_de
de Bruijn graph construction, error removal and repeat resolution (colorspace version)
- Provided by: velvet (Version: 1.2.10+dfsg1-7)
- Report a bug
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)
-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