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
- GUT_GENOME000067/
- GUT_GENOME000067_ALL_PAIRS/
- GUT_GENOME000067_CATALOG/
- README
- genomes_metadata.tsv
- bin_snps_by_source.py
- generate_catalog.py
- identify_ref_allele.py
- input_catalog_pairs.tsv
- input_all_pairs.tsv
- run_all_pairwise_analysis.sh
- run_all_snv_catalog.sh
bash run_all_snv_catalog.sh
- GUT_GENOME000067.catalog.noAuto.wtRef.tsv
- GUT_GENOME000067.continentBin.tsv
bash run_all_pairwise_analysis.sh
- GUT_GENOME000067.align_stats.tsv
- GUT_GENOME000067.snp_count.tsv