https://github.com/linsalrob/atavide_lite

A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings maybe specific for our compute resources
https://github.com/linsalrob/atavide_lite

Last synced: over 1 year ago
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A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings maybe specific for our compute resources

• Host: GitHub
• URL: https://github.com/linsalrob/atavide_lite
• Owner: linsalrob
• License: mit
• Created: 2023-07-27T13:01:25.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-10-17T21:22:51.000Z (over 1 year ago)
• Last Synced: 2024-10-20T08:16:11.091Z (over 1 year ago)
• Language: Python
• Size: 87.9 KB
• Stars: 2
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: citation.cff

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# atavide lite

A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings maybe specific for our compute resources

[atavide](https://github.com/linsalrob/atavide) is a full-fledged metagenome processing pipeline. This is a simpler version that uses either slurm scripts or PBS scripts to accomplish the same things. In this initial release, we avoided snakemake to work through the steps one at a time, although that will likely come soon.

# Pipeline steps

1. Run fastp to trim Illumina adapters

2. Use `minimap2` and `samtools` to filter out host and not host reads. Currently host reads are ignored. Host can be human or anything else.

3. Use `mmseqs easy-taxonomy` to compare not host reads to UniRef. By default we use UniRef50 but you could use any version.

4. Create a taxonomic summary for each sample and make a single `.tsv` file.

5. Connect in the subsystems from BV-BRC, and make a table that includes subsystems and taxonomic information

6. Create a subsystems taxonomy for the data

# different versions

See the verions:

   - [slurm](slurm/README.md) - designed to work on Flinders deepthought infrastructure

   - [pbs](pbs/README.md) - designed to work on the NCI infrastructrue for now

   - [minion pawsey](minion_pawsey)

Currently the pipeline depends on these software

   - fastp

   - samtools

   - minimap2

   - megahit

   - mmseqs

   - vamb

You can install all of these with:

```

mamba env create -f ~/atavide_lite/atavide_lite.yaml

```

If you use atavide light, please [cite it](citation.cff) and then please also [cite the other papers](references.bib) that describe these great tools.