1.1.1. Python dependencies¶

• snakemake >= 4.4.0
• drmaa
• sphinx
• qaa ()

1.1.2. Third party software¶

• bbmap
• fastqc
• kat
• unicycler/spades
• velvet-optimizer
• prokka
• emboss
• ratt

For qaa:

• quast
• blobtools
• qualimap
• busco
• multiqc ()
• picardtools
• samtools
• bwa and/or bowtie2

We provide Singularity recipes (one for bgrr| and one for qaa) that cover all the requirements.

If you plan to rely on your own installations, please make sure you have Python3-compatible versions, e.g. of quast and blobtools.

1.1.3. Other resources¶

• bacteria.odb9 busco database

  http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz

• a comprehensive nucleotide sequence database (including taxonomy ids) for blobtools

  e.g. NCBI nt