Fastq2Fasta

Fastq2fasta converts single or paired end fastQ(s) in a single fasta file for Blastn input. The input file(s) can be gzipped or not.

Docker

$ docker run --rm -v ${PWD}:/data guyduche/fastq2fasta [options] FastQ_1 [FastQ_2] > out.fasta

Compilation from source

Requirements

• make
• gcc
• zlib1g-dev

Compilation

$ make

Run

$ fastq2fasta [options] FastQ_1 [FastQ_2] > out.fasta

Options

Option	Description
-o FILE	File output. Default: stdout.
-h	Help

Example

FastQ

First in pair

(...)
@ERR656485.2 2 length=300
NTGGGCTAAAGGCCTTTTCCTCTATTACTTTTACCCATGCATTTAAAGTTCTAGGTGACATGGCCTGGTGTACCATTTGCCCTTGGAGATTTTGCACTATAGGATAATTTTGACTGACCTTCCCGTCAGCCCCTTTTTCCTGCTGTGTCTTTTGCTGACTTTGCTGACATTTGTTTTGTTCTTCCTCTATCTTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGATAGAGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGAAGAAAAGCAAGCAACACTAGG
+ERR656485.2 2 length=300
!8ACC@FGGGGGGGGFGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGGFGGGGFCEFFGGGGGGGGGGGFGECFFGDGGGGGGGGGGEFGGGEGGGEFGGGGGGGGEFFFGGE?FFGGGGGFFGGGGGGFGGEGGGGGFGGGGGGGGGGFGGCEGDGGGGGGGGFGGGG9EGFFEGGGGGGGGGGGFFGF;DEGGGGFGGG>868EFGGFD?FGFGG55:FDFFF>:95??A=FAFF==B=46B47).1592::EEB?25-9@CE5>=/6>E02>96>(-.((.((,(((((,((((.,)(
(...)

Second in pair

(...)
@ERR656485.2 2 length=300
NAGATAGAGGAAGAACAAAACAAATGTCAGCAAAGTCAGCAAAAGACACAGCAGGAAAAAGGGGCTGACGGGAAGGTCAGTCAAAATTATCCTATAGTGCAAAATCTCCAAGGGCAAATGGTACACCAGGCCATGTCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAGGAAAAGGCCTTTAGCCCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTCTCATTACAAAAAAAACATACACAATAAATGATATAAGCGGAATCAACAGCATGA
+ERR656485.2 2 length=300
!8A@CGGEFGFGCDFGGGGGGGGGGGGGGFGGGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGFGGFGGGGGGGGGEGFGFGGGFFGGGGGGGGFGGGGGGGGGGGGFFFFGGGGGG=FFGGFFDGGGGGGGG8FGFGGGGGGGGGFGGGGGGGGGGFDGGFGGFGGGFFFGFF8DFDFDFFFFFFFFFBCDB<@EAFB@ABAC@CDFF?4>EEFE<*>BDAFB@FFBFF>((6<5CC.;C;=D9106(.))).)-46<<))))))))))((,(-)))()((()))
(...)

Fasta output

(...)
>ERR656485.2
NTGGGCTAAAGGCCTTTTCCTCTATTACTTTTACCCATGCATTTAAAGTTCTAGGTGACATGGCCTGGTGTACCATTTGCCCTTGGAGATTTTGCACTATAGGATAATTTTGACTGACCTTCCCGTCAGCCCCTTTTTCCTGCTGTGTCTTTTGCTGACTTTGCTGACATTTGTTTTGTTCTTCCTCTATCTTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGATAGAGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGAAGAAAAGCAAGCAACACTAGG
>ERR656485.2
NAGATAGAGGAAGAACAAAACAAATGTCAGCAAAGTCAGCAAAAGACACAGCAGGAAAAAGGGGCTGACGGGAAGGTCAGTCAAAATTATCCTATAGTGCAAAATCTCCAAGGGCAAATGGTACACCAGGCCATGTCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAGGAAAAGGCCTTTAGCCCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTCTCATTACAAAAAAAACATACACAATAAATGATATAAGCGGAATCAACAGCATGA
(...)

Authors

• Aurélien Guy-Duché
• Pierre Lindenbaum

Contribute

• Issue Tracker: https://github.com/guyduche/Fastq2Fasta/issues
• Source Code: https://github.com/guyduche/Fastq2Fasta

License

The project is licensed under the MIT2 license.