RASE - Resistance-Associated Sequence Elements
January 2, 2020 ยท View on GitHub
| This repository contains the core RASE package. Other components of the software include the RASE pipeline and the RASE DB skeleton. For more information, see the RASE paper and the RASE supplementary materials. |
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Content
Introduction
This repository contains the core RASE software for rapid inference of antibiotic resistance and susceptibility using genomic neighbor typing.
Installation
-
Setup an environment
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Install RASE using PIP
pip install --upgrade git+https://github.com/c2-d2/rase
File formats
Prediction output (timeline)
Tab-separated text file with the following columns:
| column | description |
|---|---|
datetime | datetime of the read |
reads | number of processed reads |
kbps | number of processed bps (thousands) |
kkmers | number of matched k-mers (thousands) |
ks | k-mer score (proportion of matched k-mers) |
ls | lineage score |
ls_pass | lineage score interpretation, 1=passing 0=failing |
ln, alt_ln | predicted and alternative lineage |
bm, bm_{feature} | best-matching strain (nearest neighbor) and its features |
{ant}_ss | susceptibility score for the antibiotic {ant} |
{ant}_pred | prediction (score interpretation): S=susceptible, R=non-susceptible, S! and R!=low confidence calls |
{ant}_bm | resistance information for the best match, format: cat (mic) |
See an example file.
Prediction output (snapshot)
Tab-separated text file with the following columns:
| column | description |
|---|---|
taxid | taxid of a database strain, _unassigned_ for reads without any k-mer matches with the database |
lineage | lineage |
weight | weight (cumulative "number of k-mers matches divided by the the number of best matches") |
weight_norm | normalized weight |
length | cumulative "read length divided by number of matches" |
count | cumulative "count divided by number of matches" |
See an example file.
RASE DB metadata
Tab-separated text file with the following columns:
| column | description |
|---|---|
taxid | taxid of a database strain |
lineage | lineage |
order | order for plotting |
{feature} | arbitrary features (e.g., serotype or MLST) |
{ant}_mic | original MIC string (e.g., <0.03) |
{ant}_int | extracted MIC interval (0-0.03) |
{ant}_cat | resistance category (S/R/s/r) |
See an example file. Metadata files are generated in dedicated repositories (see RASE DB skeleton, S. pneumoniae RASE DB, and N. gonorrhoeae RASE DB).
RASE/BAM
File following the SAM/BAM specification, containing the following information:
| field | description |
|---|---|
QNAME | read name (ideally with the timestamp encoded) |
FLAG | 4 for unassigned, 0 otherwise |
RNAME | strain taxid or name of an internal node |
ln:i: | read length |
h1:i: | number of k-mer matches at this node |
Related repositories
- RASE supplementary. Supplementary Materials for the RASE paper, including figures, tables, experiments, and links to other related repositories.
- RASE DB skeleton. Skeleton for creating novel RASE databases.
License
MIT.