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vmatch_seq
Martin Asser Hansen edited this page Oct 2, 2015
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vmatch_seq uses vmatch to match all sequences in the stream against a specified index created either with create_vmatch_index.
The Vmatch package must be installed in order for vmatch_seq and create_vmatch_index to work.
Read more here:
... | vmatch_seq [options] -g <genome>
or
... | vmatch_seq [options] -i <index>
[-? | --help] # Print full usage description.
[-g <genome> | --genome=<genome] # Genome to vmatch.
[-i <index> | --index_name=<index>] # Custom index to vmatch.
[-c | --count] # Replace score with hit count.
[-m | --max_hits] # Skip hits with more than maximum hits (implies --count).
[-h <string> | --hamming_dist=<string>] # Allow mismatches.
[-e <string> | --edit_dist=<string>] # Allow mismatches and indels.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output stream to file - Default=STDOUT
[-v | --verbose] # Verbose output.
... | vmatch_seq -g hg18 # Match sequences in stream againt human genome.
... | vmatch_seq -g hg18 -h 1 # allowing for one mismatch.
... | vmatch_seq -g hg18 -h 5p # allowing for 5% mismatches.
... | vmatch_seq -g hg18 -e 2 # allowing for 2 mismatches or indels.
... | vmatch_seq -g hg18 -e 10p # allowing for 10% mismatches or indels.
NB! using the -h or -e switches significantly slows down vmatch_seq.
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
vmatch_seq is part of the Biopieces framework.