iqbal-lab-org

pandora

Pan-genome inference and genotyping with long noisy or short accurate reads

gramtools

Genome inference from a population reference graph

clockwork

CRyPTIC data processing pipelines

make_prg

Code to create a PRG from a Multiple Sequence Alignment file

minos

Variant call adjudication

cobs

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

varifier

Variant call verification

viridian

pling

Plasmid analysis using rearrangement distances

Mykrobe_tb_workflow

A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe

sprog

Species Probes Generator

BIGSI

BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data

cylon

Virus assembler from amplicon sequencing reads

bigsi-ebi-api

API service for EBI's BIGSI

covid-truth-datasets

SARS-CoV-2 datasets for testing pipelines

covid-truth-eval

Evaluate accuracy of covid assemblies where truth is available

minos-paper-benchmarking

QCovid

QC pipelines for sars-cov-2 sequence+consensus submitted to the ENA

cluster_vcf_records

Python package to cluster VCF records. Used by gramtools and minos

paper_gramtools_nesting

paper_pfalciparum_DBs

py-cortex-api

Python API for cortex

tb-sputum-project

Pipeline to analyse the TB sputum data

viridian_simulations_workflow

Workflow to simulate SARS-CoV-2 amplicons and reads.

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

neo4j_benchmark

pandora_gene_distance

pandora_paper_roc

paper_pandora2020_analyses

triphecta