NAME

       velvetg  -  de  Bruijn graph construction, error removal and repeat resolution (colorspace
       version)

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

       Version  1.2.09  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 OPENMP COLOR

       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

velvetg - de Bruijn graph construction, errOctoberv2013nd repeat resolution            VELVETG(1)