About

This repository include scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies. All scripts were created within the Chernevaya Taiga project funded by the Russian Science Foundation (grant 19-16-00049). The repository also contains results of the scripts application to four hybrid (illumina + ONT) assemblies of various Chernevaya Taiga soil samples.

Suggested analysis pipeline

1. Raw sequencing data quality control and quality trimming if needed. Recommended software: FastQC, Trimmomatic.
2. Metagenome assembly. Recommended software: metaSPAdes (for illumina and illumina+ONT), metaFlye (for ONT only data)
3. BGC identification. Recommended software: antiSMASH.
4. BGC summary statistics. Script: scripts/antismash_json_parser.py
5. BGC core and additional biosynthetic gene sequence extraction. Script: scripts/antismash_json_parser.py
6. BLASTing of the extracted genes against NCBI databases. Script: scripts/snakemake_blaster.sh
7. Summarizing BLAST output. Script: scripts/blast_xml_parser.py

Contact

Please send your questions, feedback, bug reports to Alexey Gurevich: aleksey.gurevich@spbu.ru or post a GitHub issue about them.