velveth - simple hashing program Version 1.2.09



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


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


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


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


: create binary CnyUnifiedSeq file (default: off)


- 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


  • directory/Roadmaps directory/Sequences

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


Copyright 2007, 2008 Daniel Zerbino ([email protected])

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 = 63 OPENMP

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


: directory name for output files


: EITHER an odd integer (if even, it will be decremented) <= 63 (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 <= 63 (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


: 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):


: File contains paired reads interleaved in the one file (default)


: Read 2 separate files for paired reads

Read type options:

-short -shortPaired -short2 -shortPaired2 -long -longPaired -reference