jvarkit
FastqToFasta
fastq -> fasta
DEPRECATED
use awk, samtools…
Usage
Usage: fastq2fasta [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
-N
fasta line length
Default: 50
-b
trim fasta header after space
Default: false
Keywords
- fastq
- fasta
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew fastq2fasta
The java jar file will be installed in the dist directory.
Source code
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite fastq2fasta ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Example
$ java -jar dist/fastq2fasta.jar -N 60 -b file.fastq.gz
>HWI-1KL149:61:D2C11TCXX:2:1213:4591:29626
GAGTTGCTTTGTTTGAATATAGGTTGACTATACGAAGTGTGCGAGGACCTGCACCACGCA
GTAGGCCAAGATCAACTGAAACAGTGCTATCTGCACGACAA
>HWI-1KL149:61:D2C11TCXX:2:1213:4525:29650
CCTAGTAGTTCGTGGCCCCGGGCCCCTACTTAAACTCCTAGAACCACTCCTAGAAAGGGG
TGTTGCAGTTCGGCTCAGTCCCCGTGGTCGACTACTGTTTC
>HWI-1KL149:61:D2C11TCXX:2:1213:4569:29706
GCGCAGAGTTGTTTTAGCTATGCTGTGTTTGCATGGTTAGGTGGTGTACCTAGTGGTTTT
CTGAGACTTCTCTGAGGTTCTTGAGTAGATTAATACATCCC
>HWI-1KL149:61:D2C11TCXX:2:1213:4594:29713