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Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

Python 113 8 Updated Jan 21, 2025

Interpretative standards for AMR genotypes

Python 15 1 Updated Jul 16, 2024

The Startup CTO's Handbook, a book covering leadership, management and technical topics for leaders of software engineering teams

10,308 499 Updated May 5, 2024

Slurm wrapper scripts

Python 9 2 Updated Feb 13, 2024

Follow up to Grace Blackwell's 661k dataset, for 2023

Python 88 6 Updated Dec 4, 2024

ENA metadata queries

Python 1 Updated Nov 7, 2023

Python3 package to handle job submission to a compute farm

Python 5 3 Updated Feb 28, 2019

A tool to find sequencing data and metadata from public databases.

Python 560 47 Updated Aug 13, 2024

A protein-centric CRISPR gRNA design tool for TArgeted Protein Engineering: please cite Anderson&Benns et al (2020) Mol Syst Biol (2020)16:e9475

Python 4 Updated May 3, 2024

Ultrafast Sample Placement on Existing Trees

C++ 124 42 Updated Nov 22, 2024

Educational blog posts for Rust beginners

Rust 7,750 412 Updated Jan 4, 2025

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

C 1,559 554 Updated Jul 27, 2024

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

Jupyter Notebook 2 Updated Dec 16, 2021

fast sequence evolution simulation for SARS-CoV-2 and similar

Python 17 5 Updated Jul 23, 2024

VGsim is a fast and scalable simulator of viral genealogies during global pandemic.

Cython 15 8 Updated Jan 23, 2025

Virus assembler from amplicon sequencing reads

Python 5 1 Updated Apr 26, 2024
Python 16 6 Updated Jan 14, 2025

ARTIC nanopore protocol for nCoV2019 novel coronavirus

Python 168 165 Updated Mar 22, 2023

Open source code for AlphaFold 2.

Python 13,109 2,317 Updated Jan 23, 2025

Downloading data from NCBI Genometrackr

Python 1 Updated Jun 9, 2021

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

C++ 83 15 Updated Jan 25, 2024

Get assembly statistics from FASTA and FASTQ files

C++ 116 23 Updated May 9, 2023

Public facing deeplift repo

Python 847 166 Updated Apr 28, 2022

Deep learning for Metagenome Assembly Error Detection

Jupyter Notebook 26 6 Updated Nov 30, 2020

GC Skew Test for Bacterial Genomes

Python 27 2 Updated Sep 29, 2022

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Go 1,352 158 Updated Jan 18, 2025

k-mer based assembly evaluation

Shell 297 21 Updated Jun 28, 2024

Phylo.IO JS tree viewer

JavaScript 28 10 Updated Aug 6, 2024

Library of sketching functions used by PopPUNK

C++ 30 8 Updated Jan 6, 2025
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