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assemble_seq_velvet
assemble_seq_velvet assembles sequence in the stream using Velvet and outputs the contig sequences from the best assembly chosen as the one with the highest N50.
A number of assemblies are created. Different k-mer lengths give very different assembly results and all uneven k-mer sizes from 19 to 31 are used per default.
An assembly directory must be speficied, and assemble_seq_velvet leaves the original assemblies files in this directory.
Consult the Velvet documentation for more information.
Velvet must be installed in order for assemble_seq_velvet to work.
Read more here:
http://www.ebi.ac.uk/~zerbino/velvet/
... | assemble_seq_velvet [options] <dir>
[-? | --help] # Print full usage description.
[-d <dir> | --dir=<dir>] # Assembly directory.
[-t <string> | --type=<string>] # Read type: short|shortPaired|long|longPaired - Default="short"
[-k <uint> | --kmer_min=<uint>] # Minimum k-mer value - Default=19
[-K <uint> | --kmer_max=<uint>] # Maximum k-mer value - Default=31
[-i <uint> | --ins_length=<uint>] # Insert length for paired end (length of reads + insert).
[-X | --clean] # Remove directory upon completed assembly.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
In the below example illustrates a de-novo assembly of a Lactococcus lactus strain. The sequences are read with read_fastq before being piped to assemble_seq_velvet. Following the assembly, the contigs are written to file in FASTA format with write_fasta and finally the contig sequences are analyzed with analyze_assembly:
read_fastq -i Lactococcus_NCDO0505.fq |
trim_seq |
assemble_seq_velvet -d Velvet -v |
write_fasta -o Lactococcus_NCDO0505.contigs |
analyze_assembly -x
N50: 5296
MAX: 35366
MIN: 50
MEAN: 533
TOTAL: 2833428
COUNT: 5308
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Note that verbose output from assemble_seq_velvet is enabled with the -v switch.
Martin Asser Hansen - Copyright (C) - All rights reserved.
May 2011
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
assemble_seq_velvet is part of the Biopieces framework.