Alignment module¶

This module contains rules for for carrying out sequence alignment, calculating summary statistics of the results, and generating plots.

Rules¶

Use MAFFT to align the combined sequence file against the project reference.

Input¶:

original – the combined sequence file generated from the combine rule
reference – the project reference sequence, provided during McCoy project creation

Config¶:

align.mafft – a list of command line arguments passed directly to MAFFT
default: ['--6merpair', '--keeplength', '--addfragments']
align.threads – the number of threads (cores) to use for a single MAFFT call
default: 4
align.resources – the resources to request when submitting to a cluster
default: {'runtime': 10, 'mem_mb': 8000}

Output¶:

the aligned version of the original input file

Params¶:

the command-line arguments passed to MAFFT (set in align.mafft config entry)

Threads¶:

set to align.threads from the config file if present, else set by the number of cores available to the workflow (up-to threads_max)

Resources¶:

set to align.resources in the project config, if present

Conda¶:

channels:
  - bioconda
  - conda-forge
dependencies:
  - mafft==7.471
  - seqkit==2.1.0

Rule alignment_stats[source]¶

Conda¶:

channels:
  - jlsteenwyk
dependencies:
  - phykit
  - jlsteenwyk-biokit

Rule pairwise_identity_histogram[source]¶

Conda¶:

channels:
  - conda-forge
dependencies:
  - python=3.9
  - numpy
  - typer
  - pandas
  - plotly
  - pip
  - pip:
    - kaleido