NAME¶

velveth - simple hashing program (colorspace version)

DESCRIPTION¶

velveth - simple hashing program Version 1.2.03

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)

-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

- 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]

Version 1.2.03

-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)

-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

- 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 = 31 OPENMP COLOR Usage: ./velveth directory hash_length {[-file_format][-read_type] 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:¶

Read type options:¶

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 = 31 OPENMP COLOR Usage: ./velveth directory hash_length {[-file_format][-read_type] 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:¶

Read type options:¶