---
name: "velveth_127_long"
section: "1"
platform: "linux"
package: "velvet-long"
version: "1.2.10+dfsg1-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/velveth_127_long"
---

# velveth\_127\_long(1)

simple hashing program (MAXKMERLENGTH = 127, LONGSEQUENCES)

## NAME

velveth\_127\_long - simple hashing program (MAXKMERLENGTH = 127, LONGSEQUENCES)

## 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

-

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

## 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 = 127 OPENMP LONGSEQUENCES

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) \<= 127 (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 \<= 127 (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**