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Trim lots of metagenomics samples all at once.

Motivation

We keep writing pipelines that start with read trimming. Rather than copy-pasting code each time, this standalone Snaketool handles our trimming needs. The tool will collect sample names and files from a directory or TSV file, optionally remove host reads, and trim with your favourite read trimmer. Read trimming methods supported so far:

Fastp
Prinseq++
BBtools for Round A/B viral metagenomics
Filtlong + Rasusa for longreads

Install

Trimnami is still in development but can be easily installed with pip:

Easy install

pip install trimnami

Developer install

git clone https://github.com/beardymcjohnface/Trimnami.git
cd Trimnami/
pip install -e .

Test

Trimnami comes with inbuilt tests which you can run to check everything works fine.

# test fastp only (default method)
trimnami test

# test all SR methods
trimnami test fastp prinseq roundAB

# test all SR methods with host removal
trimnami testhost fastp prinseq roundAB

# test nanopore method (with host removal)
trimnami testnp

Usage

Trim reads with Fastp or Prinseq++

# Fastp (default)
trimnami run --reads reads/

# Prinseq++
trimnami run --reads reads/ prinseq

# Why not both!
trimnami run --reads reads/ fastp prinseq

Include host removal

trimnami run --reads reads/ --host host_genome.fasta

Longreads with host removal. Specify 'nanopore' for targets and use the appropriate minimap preset.

trimnami run \
    --reads reads/ \
    --host host_genome.fasta \
    --minimap map-ont \
    nanopore

Parsing samples with `--reads`

You can pass either a directory of reads or a TSV file to --reads.

Directory: Trimnami will infer sample names and _R1/_R2 pairs from the filenames.
TSV file: Trimnami expects 2 or 3 columns, with column 1 being the sample name and columns 2 and 3 the reads files.

More information and examples here

Configure trimming parameters

You can customise the trimming parameters via the config file. Copy the default config file.

trimnami config

Then edit the config file trimnami.out/trimnami.config.yaml in your favourite text editor. Run trimnami like normal, or point to your custom config file if you've moved it.

trimnami run ... --configfile /my/awesome/config.yaml

Outputs

Trimmed reads will be saved in various subfolders in the output directory. e.g. if trimming with Fastp or Prinseq++, trimmed reads will be in trimnami.out/fastp/ or trimnami.out/prinseq/. Paired reads will yield three files: The R1 and R2 paired reads, and any singletons from trimming or host removal. Subsampling will produce extra files of subsampled trimmed reads. Multiqc-fastqc reports for any runs will be available in trimnami.out/reports/

Example outputs

<details> <summary>Click to expand</summary>

prinseq

trimnami.out/
└── prinseq
    ├── A13-04-182-06_TAGCTT.paired.R1.fastq.gz
    ├── A13-04-182-06_TAGCTT.paired.R2.fastq.gz
    ├── A13-04-182-06_TAGCTT.paired.S.fastq.gz
    ├── A13-12-250-06_GGCTAC.paired.R1.fastq.gz
    ├── A13-12-250-06_GGCTAC.paired.R2.fastq.gz
    ├── A13-12-250-06_GGCTAC.paired.S.fastq.gz
    └── A13-135-177-06_AGTTCC.single.fastq.gz

prinseq with fastqc reports

trimnami.out/
├── prinseq
│   ├── A13-04-182-06_TAGCTT.paired.R1.fastq.gz
│   ├── A13-04-182-06_TAGCTT.paired.R2.fastq.gz
│   ├── A13-04-182-06_TAGCTT.paired.S.fastq.gz
│   ├── A13-12-250-06_GGCTAC.paired.R1.fastq.gz
│   ├── A13-12-250-06_GGCTAC.paired.R2.fastq.gz
│   ├── A13-12-250-06_GGCTAC.paired.S.fastq.gz
│   └── A13-135-177-06_AGTTCC.single.fastq.gz
└── reports
    ├── prinseq.fastqc.html
    └── untrimmed.fastqc.html

prinseq with host removal

trimnami.out/
└── prinseq
    ├── A13-04-182-06_TAGCTT.host_rm.paired.R1.fastq.gz
    ├── A13-04-182-06_TAGCTT.host_rm.paired.R2.fastq.gz
    ├── A13-04-182-06_TAGCTT.host_rm.paired.S.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.R1.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.R2.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.S.fastq.gz
    └── A13-135-177-06_AGTTCC.host_rm.single.fastq.gz

prinseq with host removal and subsampling

trimnami.out/
└── prinseq
    ├── A13-04-182-06_TAGCTT.host_rm.paired.R1.fastq.gz
    ├── A13-04-182-06_TAGCTT.host_rm.paired.R1.subsampled.fastq.gz
    ├── A13-04-182-06_TAGCTT.host_rm.paired.R2.fastq.gz
    ├── A13-04-182-06_TAGCTT.host_rm.paired.R2.subsampled.fastq.gz
    ├── A13-04-182-06_TAGCTT.host_rm.paired.S.fastq.gz
    ├── A13-04-182-06_TAGCTT.host_rm.paired.S.subsampled.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.R1.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.R1.subsampled.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.R2.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.R2.subsampled.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.S.fastq.gz
    ├── A13-12-250-06_GGCTAC.host_rm.paired.S.subsampled.fastq.gz
    ├── A13-135-177-06_AGTTCC.host_rm.single.fastq.gz
    └── A13-135-177-06_AGTTCC.host_rm.single.subsampled.fastq.gz

</details>