Introduction

mbf-fastq-processor #

Reproducible, memory safe FastQ transformations.

Graph based description of the required transformations. Great UX without suprises.

The swiss army knife of FastQ (pre-)processing.

It filters, samples, slices, dices, analyses, demultiplexes and generally does all the things you might want to do with a set of FastQ files.

Microexample #

To process a FastQ file ‘myreads.fq’, create a report on the first 5000 reads, and write them to ‘output_1.fq’, write a toml file (input.toml) like this:

[input]
    read1 = ['myreads.fq']

[[step]]
    action = "Head"
    n = 5000

[[step]]
    action = "Report"
    infix = "report"
    json = false
    html = true 

[output]
    prefix = "output"
    format = "Raw"

Run mbf-fastq-processor input.toml, receive a nice report in output_report.html.