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ampli_clean

arc_mapper

A python tool to draw arcs between points on plots. The inspiration was to draw pairs of arcs between points on a map to show reciprocal connections

entero_nextflow

Work in progress: Very simple vp1 consensus generator.

maskara

A tool to create a coverage mask from BAM files to apply during consensus generation.

mix_finder

ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

ncov_runner

Little python wrapper to generate config.yaml files for routine use.

pangotype

A containerised version of pangolin and aln2type, providing an amalgamated output from the the two tools. Designed principally with the RIE SARS-CoV-2 sequencing effort in mind.

piranha_pan

Investigating adding mpileup functionality for SNP analysis

primalscreen

A tool to find the minimal number of primer pairs required to cover a list of snps when given a primer bed file.

rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

rampart_test

snipit

snipit: summarise snps relative to your reference sequence