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velveth

man page of velveth

velveth: simple hashing program

NAME

velveth - simple hashing program

DESCRIPTION

velveth - simple hashing program Version 1.1.02

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) 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 1.1.02 -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) 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 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: -fasta -fastq -raw -fasta.gz -fastq.gz -raw.gz -sam -bam Read type options: -short -shortPaired -short2 -shortPaired2 -long -longPaired 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 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: -fasta -fastq -raw -fasta.gz -fastq.gz -raw.gz -sam -bam Read type options: -short -shortPaired -short2 -shortPaired2 -long -longPaired VELVETH(1)
 
 
 

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