A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi all!

Inspired by something I just saw in <#C0905QCFTPE|>... what are your preprocessing steps you do for reads for any type of DNA based analyses? Please dump in the thread below :point_down:

1. FastQC
2. Adapter removal / merging plus poly-G trimmiing for Illumina 2colour chem (AdapterRemoval or fastp)
3. Post-FastQC
4. (Optional) complexity filtering (Prinseq++)
5. Host-removal (bowtie2)


ok, so we have multiple steps possible in :sarek: as you know, let me try to explain.
The whole logic with UMI is being rewritten by <@U016SFULDB8>, so I'll let him details, but it's another layer of optional step to extract the UMIs and have it properly available for downstream steps,

For the usual sarek, most of it depends on how the reads are stored, but basically if it's not a FASTQ (ie uBAM or SPRING) we convert to FASTQ.
Then we ran FASTQC.
Then optionally FASTP to trim and/or split, so we can speed up with spread the following step, and gathering after,

No removal of xenograph DNA yet, we are thinking of BBMAP for this

And then after fastp/bbmap straight into alignment?