{"id":26573237,"url":"https://github.com/linsalrob/atavide_lite","last_synced_at":"2025-03-23T00:39:53.566Z","repository":{"id":184215230,"uuid":"671497428","full_name":"linsalrob/atavide_lite","owner":"linsalrob","description":"A simpler version of atavide that relies only on slurm or PBS scripts. 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Some of the settings maybe specific for our compute resources\n\n[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.\n\n# Pipeline steps\n\n1. Run fastp to trim Illumina adapters\n2. Use `minimap2` and `samtools` to filter out host and not host reads. Currently host reads are ignored. Host can be human or anything else.\n3. Use `mmseqs easy-taxonomy` to compare not host reads to UniRef. By default we use UniRef50 but you could use any version.\n4. Create a taxonomic summary for each sample and make a single `.tsv` file.\n5. Connect in the subsystems from BV-BRC, and make a table that includes subsystems and taxonomic information\n6. Create a subsystems taxonomy for the data\n\n\n# different versions\n\nSee the verions:\n   - [slurm](slurm/README.md) - designed to work on Flinders deepthought infrastructure\n   - [pbs](pbs/README.md) - designed to work on the NCI infrastructrue for now\n   - [minion pawsey](minion_pawsey)\n\nCurrently the pipeline depends on these software\n\n   - fastp\n   - samtools\n   - minimap2\n   - megahit\n   - mmseqs\n   - vamb\n\nYou can install all of these with:\n\n```\nmamba env create -f ~/atavide_lite/atavide_lite.yaml\n```\n\n\nIf you use atavide light, please [cite it](citation.cff) and then please also [cite the other papers](references.bib) that describe these great tools.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fatavide_lite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinsalrob%2Fatavide_lite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fatavide_lite/lists"}