Provided by: velvet_1.1.07~nozlibcopy-1_amd64 bug

NAME

       velveth - simple hashing program

DESCRIPTION

       velveth - simple hashing program Version 1.1.07

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)

       -noHash
              : simply prepare Sequences file,  do  not  hash  reads  or  prepare  Roadmaps  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

   - 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 1.1.07

       -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)

       -noHash
              :  simply  prepare  Sequences  file,  do  not  hash  reads or prepare Roadmaps 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

   - 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

       Usage: ./velveth directory hash_length  {[-file_format][-read_type]  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

   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

       Usage:  ./velveth  directory  hash_length {[-file_format][-read_type] 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

   Read type options:
       -short  -shortPaired

       -short2 -shortPaired2

       -long   -longPaired

       -reference