mattheww95 Goto Github PK

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

allelecodes

Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies

appflowy

AppFlowy is an open-source alternative to Notion. You are in charge of your data and customizations. Built with Flutter and Rust.

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-coronavirus

🦠Useful projects and resources for COVID-19 (2019 novel Coronavirus)

baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics

biopython

Official git repository for Biopython (originally converted from CVS)

blend

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (preliminary version at https://arxiv.org/abs/2112.08687)

bte

Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit

bug_report

Minimal reproducible example of bug involving nested schemas

cansnper

A hierarchical genotype classifier of clonal pathogens

chewbbaca

BSR-Based Allele Calling Algorithm

cl-ctrie

lock-free, concurrent, key/value index with efficient memory-mapped persistence and fast transient storage models

cl-sam

A DNA Sequence Alignment/Map (SAM) library for Common Lisp.

codon

A high-performance, zero-overhead, extensible Python compiler using LLVM

cool-retro-term

A good looking terminal emulator which mimics the old cathode display...

coordinateconverter

covidapis

crispycody

cs-video-courses

List of Computer Science courses with video lectures.

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

daligner

Find all significant local alignments between reads

datasets

Benchmark and toy datasets

dbupdatedaemon

doom-nvim

A Neovim configuration for the advanced martian hacker

ecoli_serotyping

In silico prediction of E. coli serotype

eudyptula

www.eudyptula-challenge.org

fasta36

Git repository for FASTA36 sequence comparison software