Mohammed Alser's Projects
Conda recipes for the bioconda channel.
Bioinformatics Technology Lab common code library
The next version of bwa-mem
Fast and accurate set similarity estimation via containment min hash
Materials for Computational Metagenomics class developed for NSF TUES project
COVID-19 case count in Germany state-by-state, over time (HTTP API and CSV files)
Data from BAG Tweets made useful.
⌛ A workaround to permanently store file under the global scratch file system mounted on the Hoffman2 Cluster
GateKeeper: A New Streaming Accelerator Architecture for Fast Pre-Alignment in DNA Short Read Mapping
GEMTools main repository
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).
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.
A complete daily plan for studying to become a Google software engineer.
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)
an accurate basecaller exploiting an encoder-decoder model with monotonic attention.
Global alignment and alignment extension
Markdown Cheatsheet for Github Readme.md
A versatile pairwise aligner for genomic and spliced nucleotide sequences
It extracts the reference sequence to which a read maps, given the position in the reference sequence
Pairwise Sequence Alignment Library
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.
Succinct Data Structure Library 2.0
SDSoC™ (Software-Defined System-On-Chip) Environment Tutorials
Fast, portable C implementations of Needleman-Wunsch and Smith-Waterman sequence alignment
SeqAn's official repository.
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent