Code for analyzing population genomics in genome-resolved metagenomes
NOTE: The latest and maintained version of this software is available at: https://github.com/MrOlm/inStrain
Requires: pysam, tqdm, BioPython.
python strainRep2.py -s 5 -f 0.05 -l 0.96 sorted_indexed_bam.bam scaffolds.fasta -o output --log log.txt
python strainRep2.py -h
actually is pretty helpful, that's all of the documentation.
output: 3 tables (and a big python object). Linkage table (showing snp linkage), frequency table (showing SNPs and their frequencies), and clonality table (showing the clonality and coverage of each position - from this gene clonality can be calculated and compared to the genome average) (edited)
-s 5 requires 5 reads to confirm a SNP, you can adjust depending on your coverage. -f means minimum snp frequency of 5%, -l 0.96 means that read pairs must be 96% ID to reference. the statistics reported in the log file are also super useful