This is the command velveth_de that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
velveth_de - 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]
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 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
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