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uchime_seq
Chimeric amplicon sequences can be indentfied using uchime_seq which uses a reference database.
If a record contains SEQ_NAME and SEQ the sequence will be used to search the database to
determine if the sequence is chimeric. A CHIMERIC key is added to each of these
records denoting if the sequence was found to be chimeric or not with the values YES and NO:
SEQ_NAME: GXS0P3T01CW1VQ
SEQ: TACTGAGCTAAACCAT
SEQ_LEN: 16
CHIMERIC: YES
---
The recommended GOLD database for uchime_seq and 16S amplicon sequences can be found here:
http://drive5.com/uchime/gold.fa
Usearch must be installed in order for uchime_seq to work.
Read more here:
http://www.drive5.com/usearch/
... | uchime_seq <database>
[-? | --help] # Print full usage description.
[-d <file!> | --database=<file!>] # Database for uchime search.
[-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.
To remove chimeric sequences from a 16S amplicon dataset do this:
read_sff -ci data.sff |
uchime_seq -d gold.fa |
grab -e 'CHIMERIC == NO'
Martin Asser Hansen - Copyright (C) - All rights reserved.
November 2012
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
uchime_seq is part of the Biopieces framework.