eweitz / panagram

Panagram: Interactive, alignment-free pan-genome browser

Katie Jenike, Sam Kovaka, Shujun Ou, Stephen Hwang, Srividya Ramakrishnan, Ben Langmead, Zach Lippman, Michael Schatz

An alignment-free pan-genome viewer

Installation

> pip install git+https://github.com/kjenike/panagram.git --user

OR

> git clone --recursive https://github.com/kjenike/panagram.git
> cd panagram
> pip install .

Preprocessing

Usage:

usage: panagram index [-h] [-k int] <genomes_in>.tsv -o <out_dir>/

  Anchor KMC bitvectors to reference FASTA files to create pan-kmer bitmap

  genomes_in str        TSV file with each genome ID in the first column and the path to a
                        gzipped fasta in the second column
  -k int, --k int       K-mer (default: 21)
  -o str, --out_dir str
                        Output directory for panagram index (default: None)

Where <genome_fastas.tsv> is a tab-separated file with the first column being a genome ID containing only alphanumeric characters, and the second a path to a gzipped fasta file. Will output all files to directory named <index_dir>/.

This is a work in progress, and does not yet produce the full configuration file required to run panagram view. It does, however, perform the most computationaly intensive steps required for indexing the pan-genome.

View

Usage:

usage: panagram view [-h] <config>.txt
  Display panagram viewer

Runs a local Dash server. Browser can be viewed at http://127.0.0.1:8050/ by default.

Bitdump

Usage:

usage: panagram bitdump [-h] [-v bool] index_dir coords step
  Query pan-kmer bitmap generated by "panagram index"/

  index_dir             Panagram index directory
  coords                Coordinates to query in chr:start-end format
  step                  Spacing between output kmers (optimized for multiples
                        of 100) (default: 1)
  -v bool, --verbose bool
                        Output the full bitmap (default: False)

More information coming soon!