Pinned Repositories
GateKeeper
GateKeeper: Fast Alignment Filter for DNA Short Read Mapping
MAGNET
MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering
Genome-on-Diet
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).
Shouji
Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper (2019) by Alser et al. at https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz234/28533771/btz234.pdf
SneakySnake
SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.
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
Microbe-scope
mealser's Repositories
mealser/bioconda-recipes
Conda recipes for the bioconda channel.
mealser/btllib
Bioinformatics Technology Lab common code library
mealser/bwa-mem2
The next version of bwa-mem
mealser/CMash
Fast and accurate set similarity estimation via containment min hash
mealser/Comp_Metagenomics_resources
Materials for Computational Metagenomics class developed for NSF TUES project
mealser/covid-19-germany-gae
COVID-19 case count in Germany state-by-state, over time (HTTP API and CSV files)
mealser/covid19-cases-switzerland
Data from BAG Tweets made useful.
mealser/cronjob
⌛ A workaround to permanently store file under the global scratch file system mounted on the Hoffman2 Cluster
mealser/gemtools
GEMTools main repository
mealser/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).
mealser/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.
mealser/google-interview-university
A complete daily plan for studying to become a Google software engineer.
mealser/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)
mealser/halcyon
an accurate basecaller exploiting an encoder-decoder model with monotonic attention.
mealser/JetStream-hardware
mealser/kojix2
mealser/ksw2
Global alignment and alignment extension
mealser/markdown-cheatsheet
Markdown Cheatsheet for Github Readme.md
mealser/mealser
mealser/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
mealser/PairExtractor
It extracts the reference sequence to which a read maps, given the position in the reference sequence
mealser/parasail
Pairwise Sequence Alignment Library
mealser/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.
mealser/sdsl-lite
Succinct Data Structure Library 2.0
mealser/SDSoC-Tutorials
SDSoC™ (Software-Defined System-On-Chip) Environment Tutorials
mealser/seq-align
Fast, portable C implementations of Needleman-Wunsch and Smith-Waterman sequence alignment
mealser/Shouji
Shouji: a fast and efficient pre-alignment filter for sequence alignment
mealser/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).
mealser/Sniffles
Structural variation caller using third generation sequencing
mealser/swiss-hospital-data
Data on hospital infrastructure in Switzerland