atavide is a complete workflow for metagenomics data analysis, including QC/QA, optional host removal, assembly and cross-assembly, and individual read based annotations. We have also built in some advanced analytics including tools to assign annotations from reads to contigs, and to generate metagenome-assembled genomes in several different ways, giving you the power to explore your data!
atavide is 100% snakemake and conda, so you only need to install the snakemake workflow, and then everything else will be installed with conda.
- QC/QA with prinseq++
- optional host removal using bowtie2 and samtools, as described previously. To enable this, you need to provide a path to the host db and a host db.
- pairwise assembly of each sample using megahit
- extraction of all reads that do not assemble using samtools flags
- assembly of all unassembled reads using megahit
- compilation of all contigs into a single unified set using Flye
- comparison of reads -> contigs to generate coverage
Want something else added to the suite? File an issue on github and we'll add it ASAP!
You will need to install
- The NCBI taxonomy database somewhere
- The superfocus databases somewhere, and set the SUPERFOCUS_DB environmental variable
Everything else should install automatically.
Version 1 (earliest) Created 21st Nov 2021 at 05:26 by Rob Edwards
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Created: 21st Nov 2021 at 05:26