The load_fastq_directory function

The load_fastq_directory function is one of the main ways to get data into NGLess. It takes the name of a directory

$ find sample1

This will return a sample that contains both paired-end and single-end data:

  1. The paired-end dataset sample1/SRR8053346.pair.1.fq.gz - sample1/SRR8053346.pair.2.fq.gz
  2. The paired-end dataset sample1/SRR8053355.pair.1.fq.bz2 - sample1/SRR8053355.pair.2.fq.bz2
  3. The single-end dataset sample1/SRR8053346.single.fq.gz

Currently (as of version 1.4), NGLess supports the following

  • Extensions .gz and .bz2 are handled transparently
  • The extension (prior to the compression extension) must be either .fq or .fastq
  • Before the extension, one of .1/.2 or _1/_2 or _F/_R denotes the paired-end matching

If your data does not conform to these rules, we recommend that you use symlinks to build a directory that does conform to it.