About this repo
This repository hosts the code for SNV analysis performed in this paper:
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
Please consider cite this paper if you find this repository helpful:
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
Alexandre Almeida, Stephen Nayfach, Miguel Boland, Francesco Strozzi, Martin Beracochea, Zhou Jason Shi, Katherine S. Pollard, Donovan H. Parks, Philip Hugenholtz, Nicola Segata, Nikos C. Kyrpides, Robert D. Finn
bioRxiv 762682; doi: https://doi.org/10.1101/762682
Running the code for SNV analysis requires the following dependencies intalled in local environment:
- Python
- numpy
- MUMmer4
What's included:
Directory containing input genomes:
- GUT_GENOME000067/
Direcotry hosting intermediate files for pairwise SNV analysis and creating SNV catalogue:
- GUT_GENOME000067_ALL_PAIRS/
- GUT_GENOME000067_CATALOG/
Description:
- README
Genome metadata:
- genomes_metadata.tsv
A Python script responsible for binning SNVs based on source information, e.g. continent origin:
- bin_snps_by_source.py
A Python script for generating SNV catalogue from whole genome alignments:
- generate_catalog.py
A Python script for separating reference alleles from missing sites:
- identify_ref_allele.py
Two files containing genome pairs used for generating SNV catalogue and pairwise SNV analysis:
- input_catalog_pairs.tsv
- input_all_pairs.tsv
Two all-in-one scripts for pairwise SNV analysis and producing SNV catalogue:
- run_all_pairwise_analysis.sh
- run_all_snv_catalog.sh
Tutorial for using the code:
Generate SNV catalog:
bash run_all_snv_catalog.sh
Output files:
SNV catalog file:
- GUT_GENOME000067.catalog.noAuto.wtRef.tsv
SNV binned based on continent origin:
- GUT_GENOME000067.continentBin.tsv
Generate pairwise SNV profile:
bash run_all_pairwise_analysis.sh
Output files:
Pairwise alignment summary:
- GUT_GENOME000067.align_stats.tsv
Pairwise SNP count:
- GUT_GENOME000067.snp_count.tsv