Genotyping Python Packages

spoligotyper

In silico spoligotyping of Mycobacterium tuberculosis complex genomes (M. bovis, M. tuberculosis, ...) from reads or assemblies

circle-map

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

snpmatch

A simple python library to identify the most likely strain from the population

indelpost

Python library for simple and complex indels.

fasta2genotype

Convert STACKS fasta to many genotype formats

cellsnp

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

amira-amr

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

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.

echosv

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