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