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read-through-analysis

Analysis of read-through transcripts

repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

repo-play

Experiment with repo and GA4GH

satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing

so-ontologies

Collect of SO Ontologies

sonlib

Small general-purpose library for C and Python with an emphasis on bioinformatics.

sonlib-1

Small general purpose library for C and Python with focus on bioinformatics.

sphinx

Main repository for the Sphinx documentation builder

sqanti3

Tool for the Quality Control of Long-Read Defined Transcriptomes

sqantitools

Various tools to work with data from SQUANTI3

sunclock

Sunclock 3.57 (not written by me; formerly hosted at http://www.arvernes.com/wiki/index.php/Sunclock)

synteny-play-ground

some experimentation

t2t-chm13-gene-analysis

t2t-chm13-hub

Assembly hub for T2T CHRM13 assemblies

t2t-primates-hub

Hub for the T2T Primates Project

t2t_censat_hub

T2T Centromere hub

taffy

This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files

tebreak

Find and characterise transposable element insertions

teekesselchen

Lightroom plugin that finds duplicates by metadata

toil

Toil is a scalable, efficient, cross-platform pipeline management system, written entirely in Python, and designed around the principles of functional programming.

trackhub

create, manage, and upload track hubs for use in the UCSC genome browser

transcript-frame-tools

Various toos to validate exon frames and CDS in gene annotation (not generally useful)

twobitreader

A fast python class for reading 2-bit files (used by UCSC genome browser)

ucsc-gencode-2018

uncle_psl

A BLAT (PSL) to SAM converter.

website

The MPD website