read-fillet 0.1.0

Splitting of sequence reads by internal adapter sequence search.

Read Fillet

Installation

Read Fillet can be installed from PyPI with:

pip install read_fillet

Usage

Read Fillet is run simply with:

read_fillet <fastq_directory> 

To see more options run:

read_fillet --help

For each input fastq file found in the input directory, a file with an additional _split suffix will be output into the output directory, controlled by the --output_dir option. If not --output_dir is given then the output files are placed alongside in the input files.

The new *_split.fastq will contain two new reads for each read that was split, now with suffix _1 and _2 Reads which were not split will also be added to the new file, so that *_split.fastq can be used as a match for any downstream analysis. For example the output may look like:

@<read_id> <remaining_headers>
<sequence>
+
<quality>
@<read_id>_1 <remaining_headers>
<sequence>
+
<quality>
@<read_id>_2 <remaining_headers>
<sequence>
+
<quality>

Extra Details

The purpose of this script is to split reads that are likely to be informatic concatamers. These reads typically have an imperfect match to two neighbouring adapter sequences found next to each other.

A simplified view is the following:

Here is a read, where ">>" represents the adapter sequence and "=" represent bases from the organism of interest. The reverse adapter can typically be found in the end of a read, represented as "<<" below

A typical read, with adapters in the ends, and bases of interest in the middle

    >>=====<<

Here is a chimeric read that has not been split in the software.

        A        B
    >>=====<<>>=====<<

B can either be complementary to A, in which case they form a follow-on pair, which formed dsDNA prior to sequencing. B can also be genomically distant from A, in which case it is may also desirable to split this read to avoid chimaeras

This module will look for matches to "<<>>" like below, and split these reads out into separate parts.

Before:

    read_id: 0ae195a2-6993-4a0b-afa8-bb834f4739e3

            A        B
        >>=====<<>>=====<<
               ^--^

After:

    read_id: 0ae195a2-6993-4a0b-afa8-bb834f4739e3_1
            A
        >>=====<<

    read_id: 0ae195a2-6993-4a0b-afa8-bb834f4739e3_2
            B
        >>=====<<

Assessment

An additional assessment program read_fillet_assess is available. This requires the addition dependencies: pomoxis, samtools, and seqkit. These are most easily obtained using conda (or mamba as a faster alternative):

mamba create --name read_fillet -c bioconda seqkit samtools pomoxis python3.6
conda activate read_fillet
pip install read_fillet

Help

Licence and Copyright

© 2021- Oxford Nanopore Technologies Ltd.

read_fillet is distributed under the terms of the Mozilla Public License 2.0.

Research Release

Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.