velveth_long - Online in the Cloud

PROGRAM:

NAME

velveth_long - simple hashing program (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 ([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 = 31 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) <= 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

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