Chloroplast removal tool

This is a simple tool that removes all 16s rRNAs-like reads from a paired-end sample. By using Bowtie2 paired end reads are screened against the 16S-rRNAs from the greengenes database and removed from the samples.

Requirements

Make sure you have installed the following software (packages): Bowtie2

Instalation

pip install chfilter --user

Usage

usage: chfiler remove [-h] --paired-1 PAIRED_1 --paired-2 PAIRED_2 --out-dir OUT_DIR

optional arguments:
-h, --help           show this help message and exit
--paired-1 PAIRED_1  paired read 1
--paired-2 PAIRED_2  paired read 2
--out-dir OUT_DIR    output directory

Usage example

The directory ./test/ contains a set of files that can be used to check if the program works

chfilter remove --paired-1 ./test/r1.fq --paired-2 ./test/r2.fq --out-dir ./test/

output files

The files with filtered chloroplast reads are stored as

*.no-chl.fastq