tomdstanton

yt-dlp

A feature-rich command-line audio/video downloader

tide

🌊 The ultimate Fish prompt.

ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

miniprot

Align proteins to genomes with splicing and frameshift

zotero-folder-import

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

VIBRANT

Virus Identification By iteRative ANnoTation

pharokka

fast phage annotation program

deepbgc

BGC Detection and Classification Using Deep Learning

CIAlign

UDSMProt

Protein sequence classification with self-supervised pretraining

ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

fasten

:construction_worker: Fasten toolkit, for streaming operations on fastq files

PHANOTATE

PHANOTATE: a tool to annotate phage genomes.

abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

SKA

Split Kmer Analysis

smashpp

Find and visualize rearrangements in DNA sequences

fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

Verticall

Recombination-free trees

scanstatistics

An R package for space-time anomaly detection using scan statistics.

RFPlasmid

Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf

pp-sketchlib

Library of sketching functions used by PopPUNK

asynt

Genome alignment and synteny plots

treestructure

CaveDive

vibrio_parahaemolyticus_genomoserotyping

Kaptive database of O and K antigen clusters of Vibrio parahaemolyticus

KleborateModular

A modular rewrite of Kleborate

regentrans

regentrans: R package for investigating regional pathogen transmission using genomic data

understandingGubbins

Helper scripts to parse gubbins and BratNextGen output in conjunction with iCANDY

fastKaptive