KnuttReads2Bins performs read analysis by performing Kaiju, SSU (SINA) and Sourmash classification as well as DIAMOND BLASTX searches.

Futhermore it automatically performs assembly and binning using MEGAHIT and MetaBAT2. The resulting bins and contigs are also classified and analyzed using Sourmash, CheckM, metaQUAST and CAT/BAT.

Data from every tool is parsed and combined into .tsv files. Those files are used for one-file dashboards on every step comparing provided samples.


  1. Place your paired read files in the input/ folder.
  2. Check the config.yml
  3. Use the following schema for your read files: SAMPLE_R1.fastq.gz
  4. Run the whole workflow with:
snakemake -kpj 32 --use-conda all allReport 2>&1 | tee run.log & disown

32 is the number of vCPUs to use during the run.

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