mparker2

aria2

aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.

fast-style-transfer

TensorFlow CNN for fast style transfer ⚡🖥🎨🖼

pomegranate

Fast, flexible and easy to use probabilistic modelling in Python.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

dtaidistance

Time series distances: Dynamic Time Warping (fast DTW implementation in C)

UNCALLED

Raw nanopore signal mapper that enables real-time targeted sequencing

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

miniprot

Align proteins to genomes with splicing and frameshift

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

ncls

The Nested Containment List for Python. Basically a static interval-tree that is silly fast for both construction and lookups.

igv-jupyter

Extension for Jupyter which integrates igv.js

mashtree

:deciduous_tree: Create a tree using Mash distances

f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

pyhmmer

Cython bindings and Python interface to HMMER3.

bamsnap

clipper

A tool to identify CLIP-seq peaks

crossstitch

Code for phasing SVs with SNPs

idr

IDR

Scot_covid19

results of covid19 testing in Scotland

DNAscent

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.

TranSuite

A software suite for accurate identification, annotation, translation, and feature characterization of annotate transcripts.

sge

Snakemake profile for the (Sun) Grid Engine queueing system

SL-quant

A pipeline to quantify SL trans-splicing events from RNA-seq data

AtRTD2_translation_pipeline

seamlessf5

Helpers for smoother transitioning to multi-read FAST5 files

stringtie2-initial-release

Transcript assembly and quantification for RNA-Seq

mazter_mine

An R program to calculate cleavage efficiency in MAZTER-seq derived data

iCLIPlib

Tools for dealing with iCLIP data

ChromatineStateEnrichment