abhijeetsingh1704 / fastA2Q

simple and convenient program to convert fasta sequences to fastq sequences

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.