mealser

bioconda-recipes

Conda recipes for the bioconda channel.

btllib

Bioinformatics Technology Lab common code library

bwa-mem2

The next version of bwa-mem

CMash

Fast and accurate set similarity estimation via containment min hash

Comp_Metagenomics_resources

Materials for Computational Metagenomics class developed for NSF TUES project

covid-19-germany-gae

COVID-19 case count in Germany state-by-state, over time (HTTP API and CSV files)

covid19-cases-switzerland

Data from BAG Tweets made useful.

cronjob

⌛ A workaround to permanently store file under the global scratch file system mounted on the Hoffman2 Cluster

gemtools

GEMTools main repository

Genome-on-Diet-1

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

good.software

This is the GitHub repository for our recent study "A comprehensive analysis of the usability and archival stability of omics computational tools and resources." Please follow to the repository's wiki for more information and details on how this repository is connected to the paper.

google-interview-university

A complete daily plan for studying to become a Google software engineer.

GRIM

Source code of the processing-in-memory simulator used in the GRIM-Filter paper published at BMC Genomics in 2018: "GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping using Processing-in-Memory Technologies" (preliminary version at https://arxiv.org/pdf/1711.01177.pdf)

halcyon

an accurate basecaller exploiting an encoder-decoder model with monotonic attention.

JetStream-hardware

kojix2

ksw2

Global alignment and alignment extension

markdown-cheatsheet

Markdown Cheatsheet for Github Readme.md

mealser

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

PairExtractor

It extracts the reference sequence to which a read maps, given the position in the reference sequence

parasail

Pairwise Sequence Alignment Library

review_technology_dictates_algorithms

This is the GitHub repository for our recent study "Technology dictates algorithms : Recent developments in read alignments." Please follow to the repository's wiki for more information and details on how this repository is connected to the paper.

sdsl-lite

Succinct Data Structure Library 2.0

SDSoC-Tutorials

SDSoC™ (Software-Defined System-On-Chip) Environment Tutorials

seq-align

Fast, portable C implementations of Needleman-Wunsch and Smith-Waterman sequence alignment

Shouji

Shouji: a fast and efficient pre-alignment filter for sequence alignment

SneakySnake

The first and the only work that introduces three new efficient pre-alignment filters (SneakySnake, Snake-on-Chip, and Snake-on-GPU) that work efficiently and fast on CPU, GPU, and FPGA architectures and that greatly (by more than two orders of magnitude) expedite sequence alignment. This work is led by Alser et al. (2019).

Sniffles

Structural variation caller using third generation sequencing

swiss-hospital-data

Data on hospital infrastructure in Switzerland