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 run --rm -v ${PWD}:/data guyduche/fastq2fasta [options] FastQ_1 [FastQ_2] > out.fasta- make
- gcc
- zlib1g-dev
$ make
$ fastq2fasta [options] FastQ_1 [FastQ_2] > out.fasta| Option | Description |
|---|---|
| -o FILE | File output. Default: stdout. |
| -h | Help |
(...)
@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>(-.((.((,(((((,((((.,)(
(...)
(...)
@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<<))))))))))((,(-)))()((()))
(...)
(...)
>ERR656485.2
NTGGGCTAAAGGCCTTTTCCTCTATTACTTTTACCCATGCATTTAAAGTTCTAGGTGACATGGCCTGGTGTACCATTTGCCCTTGGAGATTTTGCACTATAGGATAATTTTGACTGACCTTCCCGTCAGCCCCTTTTTCCTGCTGTGTCTTTTGCTGACTTTGCTGACATTTGTTTTGTTCTTCCTCTATCTTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGATAGAGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGAAGAAAAGCAAGCAACACTAGG
>ERR656485.2
NAGATAGAGGAAGAACAAAACAAATGTCAGCAAAGTCAGCAAAAGACACAGCAGGAAAAAGGGGCTGACGGGAAGGTCAGTCAAAATTATCCTATAGTGCAAAATCTCCAAGGGCAAATGGTACACCAGGCCATGTCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAGGAAAAGGCCTTTAGCCCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTCTCATTACAAAAAAAACATACACAATAAATGATATAAGCGGAATCAACAGCATGA
(...)
- Aurélien Guy-Duché
- Pierre Lindenbaum
- Issue Tracker: https://github.com/guyduche/Fastq2Fasta/issues
- Source Code: https://github.com/guyduche/Fastq2Fasta
The project is licensed under the MIT2 license.
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