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agent

Identification of nucleotide accessory genomic elements in bacterial or other small genome organisms

artic_validation_tools

bcftools_filter

Tools for generating consensus sequences and genome alignments from reference-based read alignments

downsample_fastq

Set of scripts to randomly downsample fastq formatted sequence read files.

essentials_local

Command line implementation of Essentials transposon insertion sequencing analysis pipeline

fasta_alignment_gene_snps

A program to identify variants and frameshifts in nucleotide multiple alignments of a single gene sequence against a reference.

fieldbioinformatics

The ARTIC field bioinformatics pipeline

gas_scripts_reference

Scripts and reference files to type Group A Streptococcus

in_silico_pcr

Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.

minion_monitor

Scripts to offload and remotely basecall fast5 files from an Oxford Nanopore MinION run

ncov_supplemental_data

Supplemental figures and data for MedRxiv manuscript https://www.medrxiv.org/content/10.1101/2020.05.19.20107144v1

pilon_tools

A set of scripts to automate and validate assembly correction using Pilon (https://github.com/broadinstitute/pilon/wiki)

sam_to_coverage

Generates coverage statistics from sam formatted alignments

script_micro_wgs

Microbial WGS pipeline for the Northwestern SCRIPT study

snp_tools

A set of tools and add-ons for SNP analysis

spine

Identification of conserved nucleotide core genome of bacteria and other small genome organisms

spine_core_and_pangenome

Core and pangenome permutation calculator using Spine output

switchamp

Characterizing antigenic switching in Neisseria gonorrhoeae and other microbes using long-read amplicon sequencing

tis_tools

Software tools for processing sequencing data from transposon insertion sequencing experiments