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NRCan / Q2Pipe

Qiime2 based pipeline designed to facilitate and standardise ecological studies by metabarcoding using Illumina Miseq data
MIT License
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Add fastqc/falco to the importation step #3

Closed Patg13 closed 1 year ago

Patg13 commented 1 year ago

Because Qiime2 quality graph are done on a sampling of every sequences in the dataset, some samples could negatively affect the graph and give an distorted view on the dataset quality, making the trimming more prone to mistakes.

Incorporation Fastqc or Falco as an optional step during the importation step could help detect potential problems with "out-of-bound" samples.

Fastqc is the original program for quality assessment, but Falco is a C++ rewrite of it, it is faster, but does not support multithreading (truthfully, neither does Fastqc, it just launch every dataset passed as argument to a different thread), but it would be easy to implement, maybe in the Q2Pipe code or even in the Falco script itself

Being written in C++, it does not rely on java, which can be a good thing because it is lighter to install

Patg13 commented 1 year ago

Done in v0.95 Falco need some more work to reveal problematic samples, but report per sample is OK for now