{"id":26573225,"url":"https://github.com/linsalrob/atavide","last_synced_at":"2025-08-02T06:08:31.010Z","repository":{"id":119515742,"uuid":"403921714","full_name":"linsalrob/atavide","owner":"linsalrob","description":"Atavistic processing of metagenomics data. 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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!\n\n`atavide` is 100% snakemake and conda, so you only need to install the snakemake workflow, and then everything else will be installed with conda.\n\n\nIt is definitely a work in progress, but you can run it with the following command \n\n```bash\nsnakemake --configfile config/atavide.yaml -s workflow/atavide.snakefile --profile slurm\n```\n\nBut you will need a [slurm profile](https://fame.flinders.edu.au/blog/2021/08/02/snakemake-profiles-updated) to make this work!\n\n\n# Installation and getting going\n\n\n1. Clone this repository from GitHub: `git clone https://github.com/linsalrob/atavide.git`\n2. Set the location of the repository: `export ATAVIDE_DIR=$PWD/atavide/`\n3. Install a few python dependencies. You probably already have most of these, but the one that trips up is `pysam`. We're working on getting `conda` configured properly to do this automatically. `pip install -r $ATAVIDE_DIR/requirements.txt`\n4. Install the [appropriate super-focus database](https://github.com/metageni/SUPER-FOCUS/issues/66) [hint: probably version 2] and set the `SUPERFOCUS_DB` directory to [point to the location of those files](https://github.com/metageni/SUPER-FOCUS#database).\n5. Copy the [NCBI taxonomy](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/) (You really just need the [taxdump.tar.gz](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz) file), and set the `NCBI_TAXONOMY` environment variable to point to the location of those files.\n6. Have a directory of fastq files with both `_R1_` and `_R2_` files in a data directory: `$DATA_DIR/fastq` \n7. Run atavide: `cd $DATA_DIR \u0026\u0026 snakemake --configfile $ATAVIDE_DIR/atavide.yaml -s $ATAVIDE_DIR/workflow/atavide.snakefile --profile slurm`\n\n\n# Current processing steps:\n\n### Steps:\n1. QC/QA with [prinseq++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus)\n2. optional host removal using bowtie2 and samtools, [as described previously](https://edwards.flinders.edu.au/command-line-deconseq/). To enable this, you need to provide a path to the host db and a host db.\n\n### Metagenome assembly\n1. pairwise assembly of each sample using [megahit](https://github.com/voutcn/megahit)\n2. extraction of all reads that do not assemble using samtools flags\n3. assembly of all unassembled reads using [megahit](https://github.com/voutcn/megahit)\n4. compilation of _all_ contigs into a single unified set using [Flye](https://github.com/fenderglass/Flye)\n5. comparison of reads -\u003e contigs to generate coverage\n\n### MAG creation\n1. [metabat](https://bitbucket.org/berkeleylab/metabat/src/master/)\n2. [concoct](https://github.com/BinPro/CONCOCT)\n3. Pairwise comparisons using [turbocor](https://github.com/dcjones/turbocor) followed by clustering\n\n### Read-based annotations\n1. [Kraken2](https://ccb.jhu.edu/software/kraken2/)\n2. [singlem](https://github.com/wwood/singlem)\n3. [SUPER-focus](https://github.com/metageni/SUPER-FOCUS)\n4. [FOCUS](https://github.com/metageni/FOCUS)\n\nWant something else added to the suite? File an issue on GitHub and we'll add it ASAP!\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fatavide","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinsalrob%2Fatavide","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fatavide/lists"}