https://github.com/abhijeetsingh1704/fasta2q

simple and convenient program to convert fasta sequences to fastq sequences
https://github.com/abhijeetsingh1704/fasta2q

conversion fasta fasta-format fasta-sequences fastq fastq-files fastq-format fq sequence

Last synced: about 1 month ago
JSON representation

simple and convenient program to convert fasta sequences to fastq sequences

• Host: GitHub
• URL: https://github.com/abhijeetsingh1704/fasta2q
• Owner: abhijeetsingh1704
• License: lgpl-3.0
• Created: 2019-10-27T19:51:07.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2020-05-13T12:14:30.000Z (over 4 years ago)
• Last Synced: 2023-10-20T16:05:36.440Z (about 1 year ago)
• Topics: conversion, fasta, fasta-format, fasta-sequences, fastq, fastq-files, fastq-format, fq, sequence
• Language: Shell
• Homepage:
• Size: 42 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# fastA2Q

* A simple and convenient program to convert fasta sequences to fastq sequences, in casava 1.8 header format version. 

* The fastq sequence Phred quality scores will be ≥ 20 and distributed throughout the fastq sequence length, reference - https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/QualityScoreEncoding_swBS.htm

### An example of fastq header output with fastA2Q

##### @LSM:213:VGKE2RP:2:1971:12668:04830 2:N:66:CGGACGTA+GTTCACGT

```

where

@         - fastq header initial

LSM       - unique instrument name

213       - run id

VGKE2RP   - flowcell id

2         - flowcell lane

1971      - tile number within the flowcell lane

12668     - 'x'-coordinate of the cluster within the tile

04830     - 'y'-coordinate of the cluster within the tile

2         - member of a pair, 1 or 2 (paired-end or mate-pair reads only)

N         - Y if the read is filtered, N otherwise

66        - 0 when none of the control bits are on, otherwise it is an even number

CGGACGTA  - index 1 sequence

+         - connection between indexes

GTTCACGT  - index 2 sequence

```

## Usage

#### Add execution permision

```

chmod +x fastA2Q

```

#### Running the program

```

fastA2Q -i /path/input_file.fasta -o /path/output_file.fastq

```

##### License

fastA2Q is licensed under the GNU Lesser General Public License v3.0

Permissions of this copyleft license are conditioned on making available complete source code of licensed works and modifications under the same license or the GNU GPLv3. Copyright and license notices must be preserved. Contributors provide an express grant of patent rights. However, a larger work using the licensed work through interfaces provided by the licensed work may be distributed under different terms and without source code for the larger work.