Filter

filter subworkflow

Basecalled Nanopore sequencing reads can have varying levels of quality. As such, Nanopore fastq files are run through porechop to remove any remaining barcodes and adapter sequences and filtlong to reduce the sample set to the highest quality subset of reads. Illumina fastq files are run through fastp to remove poor quality reads. PHIX removal is not part of this workflow.

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Donut Falls
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flowchart LR

A[nanopore fastq] -. optional .-> B[porechop]
B --> C[filtlong]
A -. default .-> C
C --> H[gzip compression]
H --> D[filtered nanopore reads]
F[illumina fastq] --> G[fastp] 
G --> E[filtered illumina reads]

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Relevant parameters (params) and their default values

• It is recommended to adjust params.filtlong_options to fit the needs of the inputs

params.fastp_options               = ''
params.filtlong_options            = '--min_length 1000 --keep_percent 95'
params.enable_porechop             = false
params.porechop_options            = ''