velveth_63_long - simple hashing program (MAXKMERLENGTH = 63,
LONGSEQUENCES)
velveth - simple hashing program Version 1.2.09
- -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:
- velveth Assem 29 -short -fastq s_1_sequence.txt
- 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
- velveth Assem 43 -short -fastq unmapped.fna
-longPaired -fasta SangerReads.fasta
- 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 (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 = 63 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) <= 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
- filename
- : path to sequence file or - for standard input
-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
- -interleaved
- : File contains paired reads interleaved in the one file (default)
- -separate
- : Read 2 separate files for paired reads
-short -shortPaired
-short2 -shortPaired2
-long -longPaired
-reference