jvarkit

IlluminaStatsFastq

Reads filenames from stdin: Count FASTQs in Illumina Result.

Usage

Usage: ilmnfastqstats [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output zip file.
    --version
      print version and exit
    -X
      maximum number of DNA indexes to print. memory consuming if not 0.
      Default: 0

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 ilmnfastqstats

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/IlluminaStatsFastq.java

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 ilmnfastqstats ? 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

Output

the software generates a directory or a zip file.

it contains the following files:

• names.tsv : file path with sample, index, lane, side , split, file size
• counts.tsv: file path,total reads, read_fail_filter, read_do_not_fail_filter
• histopos2qual: file path, position, mean-qual, count bases (excluding read_fail_filter)
• histquals: file path, [quality[, count reads
• lengths: file path, length, count reads (excluding read_fail_filter)
• notfastq: problem with that fastq
• quals : file, mean-quality (excluding read_fail_filter)
• bases! file, A,T,G,C,N (excluding read_fail_filter)
• indexes most frequent indexes

Example

$ find dir1 dir2 -type f -name "*.fastq.gz" |\
   grep -v SAMPLE1234 |\
   java -jar dist/ilmnfastqstats.jar \
   O=OUTDIR

$ ls JETER 
bases.tsv
counts.tsv
histpos2qual.tsv
histquals.tsv
lengths.tsv
names.tsv
notfastq.tsv
quals.tsv

$ find dir1 dir2 -type f -name "*.fastq.gz" |\
   grep -v SAMPLE1234 |\
   java -jar dist/ilmnfastqstats.jar \
   O=OUTDIR.zip


$ unzip -t OUTDIR.zip 
Archive:  OUTDIR.zip
    testing: names.tsv                OK
    testing: counts.tsv               OK
    testing: quals.tsv                OK
    testing: notfastq.tsv             OK
    testing: histquals.tsv            OK
    testing: histpos2qual.tsv         OK
    testing: bases.tsv                OK
    testing: lengths.tsv              OK

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