Remove chimeric reads

Our script chimera_filter.pl wraps VSEARCH, which implements the uchime algorithm, to remove chimeric reads.

Here is an example command:

chimera_filter.pl -type 1 -db /usr/local/db/single_strand/Bacteria_RDP_trainset15_092015.fa fasta_files/*

Where "-type 1" means that any reads clearly called as chimeric AND reads that are ambiguous are filtered out.

Note that a DB file needs to be input as well. You can download the versions we use from our requirements page.

Note that it is possible that the settings of "mindiv" and "minh" (see http://www.drive5.com/usearch/manual/UCHIME_score.html) could have significant effects on results. However, so far we have found that small adjustments in these parameters has only a minor effect on sensitivity and specificity when running chimera checking for 16S sequences.

If you'd like to use USEARCH v6.1 (this is not open-source, but you can look into the license for a 32-bit version at the USEARCH website) instead of VSEARCH, you can use the older version of our script called "chimera_filter_usearch61.pl" (the options are mainly the same).

Options:

• -h, --help
  Displays the entire help documentation.

• -v, --version
  Displays version number and exits.

• --type <[0|1]>
  Non-chimeric output type, either only sequences that are clearly non-chimeric (1) or all sequences that are not called as chimeric ( 0 - includes borderline sequences, "?" in uchime output).

• --mindiv < float >
  Min % divergence between query and target sequence (default 1.5, note that this differs from the uchime default of 0.8).

• --minh < float >
  Min score to be called as chimeric (default 0.2, note that this differs from the uchime default of 0.28).

• -o, --out_dir
  Output directory for filtered fastq files. Default is "non_chimeras".

• --thread <# of CPUs>
  Using this option without a value will use all CPUs on machine, while giving it a value will limit to that many CPUs. Without option only one CPU is used.

• --keep
  Flag to indicate that temporary log files should not be removed (useful for troubleshooting). Also, will prevent the "nonchimera" and "unclear" specific fastas from being removed when type == 0.

• -log
  The location to write the log file.

• -db, --database
  Database of 16S sequences to use as a reference (UDB or FASTA file).