Genotyping Python Packages

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Circular DNA analysis tools

snpmatch

A simple python library to identify the most likely strain given the SNPs for a sample

indelpost

Python library for simple and complex indels.

amira-amr

A tool to detect acquired AMR genes directly from long read sequencing data.

cellsnp

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

echosv

A novel tool for accurately merging haplotype-based SV calls and comparing SVs across reference genomes

tblg

A command-line tool to genotype Mycobacterium tuberculosis lineage from a VCF file

massgenotyping

Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data

iscanvcfmerge

Python tool to merge cross-species Illumina iScan genotype data with a reference set of genotypes from a pre-existing source.