Description

A program that counts sequence occurrences in FASTQ files.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing output name. e.g. [ id:‘test’]

fastq{:bash}

:directory

Folder with FASTQ file(s). 2FAST2Q automatically picks up all the FASTQ files inside the provided folder.

*.{fastq,gz}

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘library_name’, multiple_features_per_read:false ]

library{:bash}

:file

.csv library file following the ´Feature_name,sequence´ or ´Feature_name,sequence1:sequence2´ format. See 2FAST2Q instructions for more information.

*.csv

Output

name:type
description
pattern

count_matrix{:bash}

meta{:bash}

:map

Groovy Map containing output name. e.g. [ id:‘test’ ]

${prefix}.csv{:bash}

:file

Count matrix csv file

stats{:bash}

meta{:bash}

:map

Groovy Map containing output name. e.g. [ id:‘test’ ]

${prefix}_stats.csv{:bash}

:file

File containing all the relevant statistics such as quality passing reads, aligned reads, total reads, and sample run times.

distribution_plot{:bash}

meta{:bash}

:map

Groovy Map containing output name. e.g. [ id:‘test’ ]

${prefix}_distribution_plot.png{:bash}

:file

Violin plot of the distribution of reads per feature across all samples.

reads_plot{:bash}

meta{:bash}

:map

Groovy Map containing output name. e.g. [ id:‘test’ ]

${prefix}_reads_plot.png{:bash}

:file

Bar plot with the distribution of reads, in absolute numbers, binned to the different quality metrics indicated in the statistics.csv

reads_plot_percentage{:bash}

meta{:bash}

:map

Groovy Map containing output name. e.g. [ id:‘test’ ]

${prefix}_reads_plot_percentage.png{:bash}

:file

Bar plot with the distribution of reads, in percentage, binned to the different quality metrics indicated in the statistics.csv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

2FAST2Q
GPL-3.0-or-later

2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.

github.com/afombravo/2FAST2Q 10.7717/peerj.14041
maintainer
Github user afombravo
get in touch
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