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bridger_assembler

Rehost of Bridger Assembler from Sourceforge

bs3

BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.

bsmap

Unofficial repo for software vendoring or packaging purposes

bsmapz

Updated and optimized fork of BSMAP

buddysuite

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

bwa-mem2

The next version of bwa-mem (WIP; not recommended for production uses at the moment)

cactus

Official home of genome aligner based upon notion of Cactus graphs

cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

calc_switcherr

callintrogressions

cambodiawgs

Workflows and analyses related to my Cambodian WGS project.

camoco

Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes.

candihap

A haplotype analysis toolkit for natural variation study.

candissr

An efficient pipeline used for identifying candidate polymorphic SSRs based on multiple assembled sequences

canu

A single molecule sequence assembler for genomes large and small.

cdhit

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

centromere_seeker

bash script to search for centromeric repeat patterns in PacBio data, using several current tools (trf and R)

cgat-flow

cgat-flow repository

cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR

chloroextractor

ciliquant

Tool to assess relative circular to linear fraction

circast

CircAST is a computational tool for circular RNA full-length assembly and quantification using RNA-Seq data.

circexplorer2

circular RNA analysis toolset

circlator

A tool to circularize genome assemblies

circompara

A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

circrnafisher

A systematic computational approach for de novo circular RNA identification

circrnawrap

a cocktail for circRNA analysis

circrna_finder

Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).

circsplice

CircSplice

circtest

CircRNA testing and ploting R package