# Input Data

# Read length

Reads must be at least 30 base pairs in length for alignment. By default, the qc module removes reads <30bp.

# Compression

Harpy generally doesn't require the input sequences to be in gzipped/bgzipped format, but it's good practice to compress your reads anyway. Compressed files are expected to end with the extension .gz .

# Naming conventions

Unfortunately, there are many different ways of naming FASTQ files, which makes it difficult to accomodate every wacky iteration currently in circulation. While Harpy tries its best to be flexible, there are limitations. To that end, for the deumultiplex , qc , and align modules, the most common FASTQ naming styles are supported:

• sample names: a-z 0-9 . _ - case insensitive
  • you can mix and match special characters, but that's bad practice and not recommended
  • examples: Sample.001, Sample_001_year4, Sample-001_population1.year2 <- not recommended
• forward: _F .F _1 .1 _R1_001 .R1_001 _R1 .R1
• reverse: _R .R _2 .2 _R2_001 .R2_001 _R2 .R2
• fastq extension: .fq .fastq case insensitive
• gzipped: supported and recommended
• not gzipped: supported

You can also mix and match different formats and styles within a given directory, although again, this isn't recommended. As a good rule of thumb for any computational work, you should be deliberate and consistent in how you name things.