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baseballcap

BaseballCap is an RNA-seq Junction Read Aligner based on the Burrow-Wheeler Transform (BWT) with Last-First (LF) mapping, created as a final project for a bioinformatics course. It is meant to be a simple, crude approximation of the popular tool TopHat, hence the name BaseballCap (a "poor man's TopHat")

bioconda-recipes

Conda recipes for the bioconda channel.

conky_wunderlist

cse182

CSE 182 at UCSD (Spring 2018)

fastq_set

Tools for working FASTQ files from sequencers (R1/R2/I1/I2)

hapcut2

Performs haplotype assembly from genomic DNA sequence reads for a single individual using a maximum-likelihood based approach. Performs well on diverse NGS technologies, including long read data and Hi-C.

longshot

diploid SNV caller for error-prone reads

longshot_study

This repository contains a Snakemake recipe to recreate the Longshot study

martian-rust

Adapter for writing Martian stages in Rust

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

rust-spoa

Rust crate with bindings and interface to the SPOA library for generating consensus sequences.

rust-toolbox

Rust utility code

sissor

Scripts for analysis of SISSOR data.

talon_scripts_public

a single source of application-specific scripts