NAME

       velveth - simple hashing program (colorspace version)

DESCRIPTION

       velveth - simple hashing program Version 1.2.09

OPTIONS

       -strand_specific
              : for strand specific transcriptome sequencing data (default: off)

       -reuse_Sequences
              :  reuse Sequences file (or link) already in directory (no need to provide original
              filenames in this case (default: off)

       -reuse_binary
              : reuse binary sequences file (or link) already in directory (no  need  to  provide
              original filenames in this case (default: off)

       -noHash
              :  simply  prepare  Sequences  file,  do  not  hash  reads or prepare Roadmaps file
              (default: off)

       -create_binary
              : create binary CnyUnifiedSeq file (default: off)

       Synopsis:

   - Short single end reads:
              velveth Assem 29 -short -fastq s_1_sequence.txt

   - Paired-end short reads (remember to interleave paired reads):
              velveth Assem 31 -shortPaired -fasta interleaved.fna

       - Paired-end short reads (using separate files for the paired reads)

              velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

   - Two channels and some long reads:
              velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta

   - Three channels:
              velveth Assem 35  -shortPaired  -fasta  pe_lib1.fasta  -shortPaired2  pe_lib2.fasta
              -short3 se_lib1.fa

   Output:
              directory/Roadmaps directory/Sequences

              [Both files are picked up by graph, so please leave them there]

       Version 1.2.09

       -strand_specific
              : for strand specific transcriptome sequencing data (default: off)

       -reuse_Sequences
              :  reuse Sequences file (or link) already in directory (no need to provide original
              filenames in this case (default: off)

       -reuse_binary
              : reuse binary sequences file (or link) already in directory (no  need  to  provide
              original filenames in this case (default: off)

       -noHash
              :  simply  prepare  Sequences  file,  do  not  hash  reads or prepare Roadmaps file
              (default: off)

       -create_binary
              : create binary CnyUnifiedSeq file (default: off)

       Synopsis:

   - Short single end reads:
              velveth Assem 29 -short -fastq s_1_sequence.txt

   - Paired-end short reads (remember to interleave paired reads):
              velveth Assem 31 -shortPaired -fasta interleaved.fna

       - Paired-end short reads (using separate files for the paired reads)

              velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

   - Two channels and some long reads:
              velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta

   - Three channels:
              velveth Assem 35  -shortPaired  -fasta  pe_lib1.fasta  -shortPaired2  pe_lib2.fasta
              -short3 se_lib1.fa

   Output:
              directory/Roadmaps directory/Sequences

              [Both files are picked up by graph, so please leave them there]

COPYRIGHT

       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: ./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved]
       filename1 [filename2 ...]} {...} [options]

       directory
              : directory name for output files

       hash_length
              :  EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be
              reduced) : OR: m,M,s where m  and  M  are  odd  integers  (if  not,  they  will  be
              decremented) with m < M <= 31 (if above, will be reduced)

              and s is a step (even number). Velvet will then hash from k=m to k=M with a step of
              s

       filename
              : path to sequence file or - for standard input

   File format options:
       -fasta  -fastq  -raw    -fasta.gz       -fastq.gz       -raw.gz -sam    -bam    -fmtAuto

              (Note: -fmtAuto will detect fasta or fastq, and will try the following programs for
              decompression : gunzip, pbunzip2, bunzip2

   File layout options for paired reads (only for fasta and fastq formats):
       -interleaved
              : File contains paired reads interleaved in the one file (default)

       -separate
              : Read 2 separate files for paired reads

   Read type options:
       -short  -shortPaired

       -short2 -shortPaired2

       -long   -longPaired

       -reference

       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: ./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved]
       filename1 [filename2 ...]} {...} [options]

       directory
              : directory name for output files

       hash_length
              :  EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be
              reduced) : OR: m,M,s where m  and  M  are  odd  integers  (if  not,  they  will  be
              decremented) with m < M <= 31 (if above, will be reduced)

              and s is a step (even number). Velvet will then hash from k=m to k=M with a step of
              s

       filename
              : path to sequence file or - for standard input

   File format options:
       -fasta  -fastq  -raw    -fasta.gz       -fastq.gz       -raw.gz -sam    -bam    -fmtAuto

              (Note: -fmtAuto will detect fasta or fastq, and will try the following programs for
              decompression : gunzip, pbunzip2, bunzip2

   File layout options for paired reads (only for fasta and fastq formats):
       -interleaved
              : File contains paired reads interleaved in the one file (default)

       -separate
              : Read 2 separate files for paired reads

   Read type options:
       -short  -shortPaired

       -short2 -shortPaired2

       -long   -longPaired

       -reference