An index describing the public and private repositories created by Banfield lab members.

Please slack an administrator with your username and the project name below to get access to a listed private repository.

• EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

• dRep - Dereplication of microbial genomes

• iRep - estimating bacteria replication rates based on population genome copy number variation

• DAS Tool - Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy

• fix_assembly_errors - This repository contains scripts for microbial genome sequence curation. The key scripts are re_assemble_errors.py, ra2.py, and mapped.py.

• pipeCoverage - Quickly calculate coverage of sequences in a .sam file while retaining breadth information

• get_ncbi_genomes - Download genomes from NCBI Genome database using compound queries.