https://github.com/opengene/pecheck
check paired-end FASTQ data integrity
https://github.com/opengene/pecheck
bioinformatics check consistence fastq identical illumina integrity paired-end pe
Last synced: 3 months ago
JSON representation
check paired-end FASTQ data integrity
- Host: GitHub
- URL: https://github.com/opengene/pecheck
- Owner: OpenGene
- License: mit
- Created: 2018-07-27T04:44:00.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2018-08-01T02:18:58.000Z (about 7 years ago)
- Last Synced: 2025-04-10T09:54:06.304Z (6 months ago)
- Topics: bioinformatics, check, consistence, fastq, identical, illumina, integrity, paired-end, pe
- Language: C
- Size: 83 KB
- Stars: 6
- Watchers: 7
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# pecheck
A tool to check paired-end FASTQ data integrity
# usage
Just specify the read1 file by `-i` and the read2 file by `-I`. The input file can be gzipped (i.e. R1.fq.gz).
```
pecheck -i R1.fq -I R2.fq
```
A JSON report will be then generated. If the check is passed, the JSON result will be like:
```json
{
"result":"passed",
"message":"",
"read1_num":1000,
"read2_num":1000,
"read1_bases":108040,
"read2_bases":109141
}
```
And if it's failed, the JSON result will be like:
```json
{
"result":"failed",
"message":"Numbers of read1 and read2 are different",
"read1_num":999,
"read2_num":1000,
"read1_bases":107923,
"read2_bases":109141
}
```
The file name of the JSON report is `pecheck.json` by default, and it can be specified by `-j`. The JSON result is also printed on the terminal (STDOUT).
# get pecheck
## download binary
This binary is only for Linux systems: http://opengene.org/pecheck/pecheck
```shell
# this binary was compiled on CentOS, and tested on CentOS/Ubuntu
wget http://opengene.org/pecheck/pecheck
chmod a+x ./pecheck
```
## or compile from source
```shell
# get source (you can also use browser to download from master or releases)
git clone https://github.com/OpenGene/pecheck.git
# build
cd pecheck
make
# Install
sudo make install
```