martinghunt Goto Github PK

gpas-covid-testsets

A series of SARS-CoV-2 development testsets for the different pipelines available in GPAS

gramtools

Genome inference from a population reference graph

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

homebrew-python

:snake: Python formulae for Homebrew

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

iva

de novo virus assembler of Illumina paired reads

iva-publication

Supplementary scripts and data for the IVA publication

make_prg

Code to create a PRG from a Multiple Sequence Alignment file

mccortex

Cortex on steroids: for larger populations with better assembly

minimap2

A fast pairwise aligner for genomic and spliced nucleotide sequences

minos

Variant call adjudication

minos-paper-benchmarking

mykrobe

Cli tools for Mykrobe atlas and Mykrobe predictor

mykrobe-data

Data for mykrobe command line tool

mykrobe-lineage-test

Test species and lineage calls made by mykrobe

mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop

pacbio-14-nctc-assemblies

14 NCTC samples for testing PacBio assemblers

pathfind

Modularised versions of *find scripts

pathogen-informatics-training

pathogens-vm

To build a virtual machine with some Sanger pathogens software installed

perl-intro

preprocessing

Mycobacterial pre-processing pipeline

primer3tools

Design PCR primers and check uniqueness across multiple genomes

py-cortex-api

Python API for cortex

pymummer

Python3 module for running MUMmer and reading the output

rapid_annotation_transfer_tool

RATT: A tool for transferring genomic annotations between genomes

read-it-and-keep

Read contamination removal

scaffolder-evaluation

Wrapper scripts to run genome assembly scaffolding tools and scripts to analyse the output for accuracy.

simutator

Simulate mutations in genomes

singularity_preexec_test

Singularity preexec test script for EBI clusters