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apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

bamsifter

normalizes coverage depth by position-specific read sampling in a bam file to give a target max depth

bioruby

bioruby

bioruby-use

Codes using bioruby library

cairo

R graphics device using cairo graphics library for creating high-quality output

canu

A single molecule sequence assembler for genomes large and small.

crisporwebsite

All source code of the crispor.org website

depthhist

Calculate clone depth histogram in wig format from SAM/BAM

duplex-sequencing

falcon

FALCON: experimental PacBio diploid assembler

ffton

Fast File Transfer over NAT

hypermut

A program to identify fragments with multiple substitutions and collect relevant statistics

jbrowse

A modern genome browser built with JavaScript and HTML5.

jin-annot

Scripts for annotating a genome with RNA-seq and Protein sequence data.

klab

Kasahara lab. public repository.

minialign

fast and accurate alignment tool for PacBio and Nanopore long reads

novoplasty

NOVOPlasty - The organelle assembler

phylotrees.jl

Phylogenetic trees in Julia

platanus_b

De novo genome assembler for bacterial genomes

rails-contigdb_pame3

rpostgresql

Automatically exported from code.google.com/p/rpostgresql

ruby-dbi

Ruby/DBI, a database abstraction layer and interface

scd30-raspberry-pi

Python library for Raspberry pi and the SCD30 CO2 sensor

solid

Software tools for processing SOLiD sequence data

tcc

R package for tag count comparison

tgew

A set of small scripts that make things easier for users of Sun Grid Engine

umi_sc

utgb

University of Tokyo Genome Browser