xxzou

adamcatley.github.io

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

polars

Dataframes powered by a multithreaded, vectorized query engine, written in Rust

duckdb

DuckDB is an analytical in-process SQL database management system

primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).

primer3-py

Simple oligo analysis and primer design

ColabFold

Making Protein folding accessible to all!

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

PrimerServer2

PrimerServer2: a high-throughput primer design and specificity-checking platform

superfile

Pretty fancy and modern terminal file manager

micropython

MicroPython - a lean and efficient Python implementation for microcontrollers and constrained systems

minion_monitor

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

MultiplexNanopore

Circuitseq

Nanopore Plasmid Sequencing

plassembler

Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

canu

A single molecule sequence assembler for genomes large and small.

stylo

Nanopore assembly workflow from basecalled reads to polished assembly plus assembly QC, metrics, and plasmid replicon detection

Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

Flye

De novo assembler for single molecule sequencing reads using repeat graphs

svgedit

Powerful SVG-Editor for your browser

ultraplex

Ultra-fast 5' and 3' demultiplexer

UltraPlexer

The UltraPlexer is a kmer-based tool that allows assigning non-barcoded long-read sequences generated by the Oxford Nanopore Technology to isolates, by matching them to barcoded short-read sequences generated by Illumina Technology.

dorado

Oxford Nanopore's Basecaller

Porechop

adapter trimmer for Oxford Nanopore reads

awesome-nanopore

A curated list of awesome nanopore analysis tools.

RcloneTray

Simple cross-platform GUI for Rclone

rclone-webui-react

A full fledged UI for the rclone cloud sync tool

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html