[](https://github.com/beardymcjohnface/Snaketool)
[](https://opensource.org/license/mit/)
[](https://pypi.org/project/trimnami/)
[](http://bioconda.github.io/recipes/trimnami/README.html)
[](https://github.com/beardymcjohnface/Trimnami/actions/workflows/python-app.yml)
[](https://github.com/beardymcjohnface/Trimnami/actions/workflows/trimnami-build-envs.yml)
[](https://codecov.io/gh/beardymcjohnface/Trimnami)
---
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__
```shell
pip install trimnami
```
__Developer install__
```shell
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.
```shell
# 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++
```shell
# Fastp (default)
trimnami run --reads reads/
# Prinseq++
trimnami run --reads reads/ prinseq
# Why not both!
trimnami run --reads reads/ fastp prinseq
```
Include host removal
```shell
trimnami run --reads reads/ --host host_genome.fasta
```
Longreads with host removal.
Specify 'nanopore' for targets and use the appropriate minimap preset.
```shell
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](https://gist.github.com/beardymcjohnface/bb161ba04ae1042299f48a4849e917c8#file-readme-md)__
## Configure trimming parameters
You can customise the trimming parameters via the config file.
Copy the default config file.
```shell
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.
```shell
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
```text
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
```text
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
```text
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
```text
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>
Raw data
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"author_email": "beardymcjohnface@gmail.com",
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"description": "\n\n[](https://github.com/beardymcjohnface/Snaketool)\n[](https://opensource.org/license/mit/)\n[](https://pypi.org/project/trimnami/)\n[](http://bioconda.github.io/recipes/trimnami/README.html)\n\n[](https://github.com/beardymcjohnface/Trimnami/actions/workflows/python-app.yml)\n[](https://github.com/beardymcjohnface/Trimnami/actions/workflows/trimnami-build-envs.yml)\n[](https://codecov.io/gh/beardymcjohnface/Trimnami)\n\n\n---\n\nTrim lots of metagenomics samples all at once.\n\n## Motivation\n\nWe keep writing pipelines that start with read trimming.\nRather than copy-pasting code each time,\nthis standalone Snaketool handles our trimming needs.\nThe tool will collect sample names and files from a directory or TSV file,\noptionally remove host reads, and trim with your favourite read trimmer.\nRead trimming methods supported so far:\n\n- Fastp\n- Prinseq++\n- BBtools for Round A/B viral metagenomics\n- Filtlong + Rasusa for longreads\n\n## Install\n\nTrimnami is still in development but can be easily installed with pip:\n \n__Easy install__\n\n```shell\npip install trimnami\n```\n\n__Developer install__\n```shell\ngit clone https://github.com/beardymcjohnface/Trimnami.git\ncd Trimnami/\npip install -e .\n```\n\n## Test\n\nTrimnami comes with inbuilt tests which you can run to check everything works fine.\n\n```shell\n# test fastp only (default method)\ntrimnami test\n\n# test all SR methods\ntrimnami test fastp prinseq roundAB\n\n# test all SR methods with host removal\ntrimnami testhost fastp prinseq roundAB\n\n# test nanopore method (with host removal)\ntrimnami testnp\n```\n\n## Usage\n\nTrim reads with Fastp or Prinseq++\n\n```shell\n# Fastp (default)\ntrimnami run --reads reads/\n\n# Prinseq++\ntrimnami run --reads reads/ prinseq\n\n# Why not both!\ntrimnami run --reads reads/ fastp prinseq\n```\n\nInclude host removal\n\n```shell\ntrimnami run --reads reads/ --host host_genome.fasta\n```\n\nLongreads with host removal.\nSpecify 'nanopore' for targets and use the appropriate minimap preset.\n\n```shell\ntrimnami run \\\n --reads reads/ \\\n --host host_genome.fasta \\\n --minimap map-ont \\\n nanopore\n```\n\n## Parsing samples with `--reads`\n\nYou can pass either a directory of reads or a TSV file to `--reads`.\n - __Directory:__ Trimnami will infer sample names and \\_R1/\\_R2 pairs from the filenames.\n - __TSV file:__ Trimnami expects 2 or 3 columns, with column 1 being the sample name and columns 2 and 3 the reads files.\n\n__[More information and examples here](https://gist.github.com/beardymcjohnface/bb161ba04ae1042299f48a4849e917c8#file-readme-md)__\n\n## Configure trimming parameters\n\nYou can customise the trimming parameters via the config file.\nCopy the default config file.\n\n```shell\ntrimnami config\n```\n\nThen edit the config file `trimnami.out/trimnami.config.yaml` in your favourite text editor.\nRun trimnami like normal, or point to your custom config file if you've moved it.\n\n```shell\ntrimnami run ... --configfile /my/awesome/config.yaml\n```\n\n## Outputs\n\nTrimmed reads will be saved in various subfolders in the output directory.\ne.g. if trimming with Fastp or Prinseq++, \ntrimmed reads will be in `trimnami.out/fastp/` or `trimnami.out/prinseq/`.\nPaired reads will yield three files: \nThe R1 and R2 paired reads, and any singletons from trimming or host removal.\nSubsampling will produce extra files of subsampled trimmed reads.\nMultiqc-fastqc reports for any runs will be available in `trimnami.out/reports/`\n\n### Example outputs\n<details>\n <summary>Click to expand</summary>\n\nprinseq\n\n```text\ntrimnami.out/\n\u2514\u2500\u2500 prinseq\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.paired.R1.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.paired.R2.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.paired.S.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.paired.R1.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.paired.R2.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.paired.S.fastq.gz\n \u2514\u2500\u2500 A13-135-177-06_AGTTCC.single.fastq.gz\n```\n\nprinseq with fastqc reports\n\n```text\ntrimnami.out/\n\u251c\u2500\u2500 prinseq\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 A13-04-182-06_TAGCTT.paired.R1.fastq.gz\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 A13-04-182-06_TAGCTT.paired.R2.fastq.gz\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 A13-04-182-06_TAGCTT.paired.S.fastq.gz\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 A13-12-250-06_GGCTAC.paired.R1.fastq.gz\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 A13-12-250-06_GGCTAC.paired.R2.fastq.gz\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 A13-12-250-06_GGCTAC.paired.S.fastq.gz\n\u2502\u00a0\u00a0 \u2514\u2500\u2500 A13-135-177-06_AGTTCC.single.fastq.gz\n\u2514\u2500\u2500 reports\n \u251c\u2500\u2500 prinseq.fastqc.html\n \u2514\u2500\u2500 untrimmed.fastqc.html\n\n```\n\nprinseq with host removal\n\n```text\ntrimnami.out/\n\u2514\u2500\u2500 prinseq\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.R1.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.R2.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.S.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.R1.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.R2.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.S.fastq.gz\n \u2514\u2500\u2500 A13-135-177-06_AGTTCC.host_rm.single.fastq.gz\n```\n\nprinseq with host removal and subsampling\n\n```text\ntrimnami.out/\n\u2514\u2500\u2500 prinseq\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.R1.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.R1.subsampled.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.R2.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.R2.subsampled.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.S.fastq.gz\n \u251c\u2500\u2500 A13-04-182-06_TAGCTT.host_rm.paired.S.subsampled.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.R1.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.R1.subsampled.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.R2.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.R2.subsampled.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.S.fastq.gz\n \u251c\u2500\u2500 A13-12-250-06_GGCTAC.host_rm.paired.S.subsampled.fastq.gz\n \u251c\u2500\u2500 A13-135-177-06_AGTTCC.host_rm.single.fastq.gz\n \u2514\u2500\u2500 A13-135-177-06_AGTTCC.host_rm.single.subsampled.fastq.gz\n```\n</details>\n\n",
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