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Snakemake workflow: accel-amplicon-trimming

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This workflow performs read trimming on Accel Amplicon Panel data, using the recommended guidelines provided by Swift

Authors

Patrik Smeds (@smeds)

Requirements

Samples have to be Paired-End Illumina sequences.

Usage

Step 1: Install workflow

If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.

In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, once available, its DOI.

Step 2: Configure workflow

Configure the workflow according to your needs by editing the config.yaml and the sample sheet samples.tsv.

Config.yaml

The following entries are expected in the config file

illuminaclip_file: /path/to/illumina.fa

accel_panels:
  panel1:
    5p_primer_file: /path/to/5p_primers.fa
    3p_primer_file: /path/to/3p_primers.fa
  panel2:
    5p_primer_file: /path/to/5p_primers.fa
    3p_primer_file: /path/to/3p_primers.fa

Sample.tsv

Example of a sample.tsv file (columns need to be tab separated)

sample     panel
sample1    panel1
sample2    panel2

The panel column must contain a panel name that can be found in the accel_panels entry in the config.yaml

unit.tsv

Example of a units.tsv file (columns need to be tab separated)

sample     unit     fq1                fq2
sample1    lane1    /path/to/sample1.R1.fastq   /path/to/sample1.R2.fastq
sample2    lane1    /path/to/sample2.R1.fastq   /path/to/sample2.R2.fastq

There cane be multiple lanes or replicates for the same sample.

Step 3: Execute workflow

Test your configuration by performing a dry-run via

snakemake -n

Execute the workflow locally via

snakemake --cores $N

using $N cores or run it in a cluster environment via

snakemake --cluster qsub --jobs 100

or

snakemake --drmaa --jobs 100

See the Snakemake documentation for further details.