chfilter 1.3

## 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
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### Instalation

pip install chfilter --user

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### 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
clremove clear --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