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velvetg

man page of velvetg

velvetg: de Bruijn graph construction, error removal and repeat resolution

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) -long_cov_cutoff <floating-point>: removal of nodes with low long-read coverage AFTER tour bus (default: no removal) 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: 5) -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) -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) 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 1.1.02 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) -long_cov_cutoff <floating-point>: removal of nodes with low long-read coverage AFTER tour bus (default: no removal) 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: 5) -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) -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) 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,2011or removal and repeat VELVETG(1)
 
 
 

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