Beast code in Giters

Ola Brynildsrud's starred repositories

big-list-of-naughty-strings

The Big List of Naughty Strings is a list of strings which have a high probability of causing issues when used as user-input data.

Language:PythonMIT46163 850 99

teams-for-linux

Unofficial Microsoft Teams for Linux client

Language:JavaScriptGPL-3.02830 54 870

seqtk

Toolkit for processing sequences in FASTA/Q formats

Language:CMIT1376 62 173

ncov

Nextstrain build for novel coronavirus SARS-CoV-2

Language:PythonMIT1354 77 419

gget

🧬 gget enables efficient querying of genomic reference databases

Language:PythonBSD-2-Clause933 11 68

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Language:C++MIT776 46 687

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Language:PerlGPL-2.0470 30 581

Roary

Rapid large-scale prokaryote pan genome analysis

Language:PerlNOASSERTION316 29 397

shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

Language:PerlGPL-3.0210 17 174

mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Language:PythonApache-2.0118 12 143

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

Language:JavaScriptMIT115 11 149

mccortex

De novo genome assembly and multisample variant calling

Language:CMIT113 15 91

learning_bam_file

Learning the Sequence Alignment/Map format

Language:PerlMIT110 80

treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

Language:RNOASSERTION94 13 76

ggCaller

Bifrost graph gene caller.

Language:C++MIT86 3 29

BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

Language:PerlNOASSERTION58 9 984

Verticall

Recombination-free trees

Language:PythonGPL-3.056 4 4

PyVCF3

A Variant Call Format reader for Python.

Language:PythonNOASSERTION52 4 8

IS_mapper

IS mapping software

Language:PythonNOASSERTION51 7 47

LS-BSR

Large scale Blast Score Ratio (BSR) analysis

Language:Pep8GPL-3.038 6 29

EToKi

all methods related to Enterobase

Language:PythonGPL-3.038 10 12