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Seqfu

note

Manipulate FASTA/FASTQ files.

https://telatin.github.io/seqfu2

Supported commands:

  • stats:

seqfu stats​

Input files​

seqfu stats can generated reports in multiple formats, see https://telatin.github.io/seqfu2/tools/stats.html. Only TSVs with headers (default seqfu stats output) are currently detected and parsed by MultiQC.

note

seqfu stats has a --multiqc option that generates a _mqc.txt file can be used with MuliQC as custom content. This is different from this module which enables additional features.

Configuration​

Sample names are automatically extracted from the "File" columns by default. If you only have one sample per file and prefer to use the filename as the sample name instead, you can set the global use_filename_as_sample_name option to true or list seqfu under it.

File search patterns​

seqfu/stats:
  contents: "File\t#Seq\tTotal bp\tAvg\tN50\tN75\tN90\tauN\tMin\tMax"
  num_lines: 1