https://github.com/karel-brinda/phylogenetic-compression-supplement
Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"
https://github.com/karel-brinda/phylogenetic-compression-supplement
assemblies bacteria bioinformatics compression genomes indexing k-mers mof phylogenetic-compression phylogeny
Last synced: 3 months ago
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Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"
- Host: GitHub
- URL: https://github.com/karel-brinda/phylogenetic-compression-supplement
- Owner: karel-brinda
- License: mit
- Created: 2020-10-23T17:42:27.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-11-21T11:35:05.000Z (6 months ago)
- Last Synced: 2024-11-21T12:27:57.606Z (6 months ago)
- Topics: assemblies, bacteria, bioinformatics, compression, genomes, indexing, k-mers, mof, phylogenetic-compression, phylogeny
- Language: Python
- Homepage: http://brinda.eu/mof
- Size: 34 MB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Phylogenetic compression - supplementary files
Supplementary files for the paper
* K. Břinda, L. Lima, S. Pignotti, N. Quinones-Olvera, K. Salikhov, R. Chikhi, G. Kucherov, Z. Iqbal, and M. Baym, **Efficient and robust search of microbial genomes via Phylogenetic Compression**, bioRxiv 2023.04.15.536996, 2023. https://doi.org/10.1101/2023.04.15.536996
## Table of Contents
* [BIGSIdata](#bigsidata)
* [GISP](#gisp)
* [NCTC3k](#nctc3k)
* [SC2](#sc2)
## BIGSIdata
**[decompress-bigsi-data](BIGSIdata/decompress-bigsi-data)**
Program to decompress phylogenetically compressed de Bruijn graphs from Fig 2.
## GISP
* [Results of the ngono scaling experiment](GISP/gisp_ngen_scaling.tsv)
## NCTC3k
* [Results of the NCTC3k scaling experiment](NCTC3k/nctc3k_ngen_scaling.tsv)
## SC2
* [Results of the SC2 scaling experiment](NCTC3k/nctc3k_ngen_scaling.tsv)