Illuminafastqstats

motivation

Generate Statistics for FASTQs.

History

• 2013-10-31 : added options EXCLUDE_REGEXES, INCLUDE_REGEXES, COUNT_INDEX

Compilation

see also Compilation

ant ilmnfastqstats

Options

Option	Description
IN=File	Directories to process Required.
OUT=File	Output Name (Directory or .zip file) Required.
EXCLUDE_REGEXES=String	regular expression exclude pattern This option may be specified 0 or more times.
INCLUDE_REGEXES=String	regular expression include pattern This option may be specified 0 or more times.
COUNT_INDEX=Integer	maximum number of DNA indexes to print. memory consuming if not 0.

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

$ java -jar dist/ilmnfastqstats.jar \
   I=dir1 I=dir2  \
   O=OUTDIR

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

$ java -jar dist/ilmnfastqstats.jar \
   I=dir1 I=dir2  \
   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