memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

• UpdatedFeb 20, 2025
• C++

RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published athttps://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).

• UpdatedDec 9, 2024
• C

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGABhttps://doi.org/10.1093/nargab/lqad004)

• UpdatedMay 10, 2023
• C

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

• UpdatedMar 5, 2025
• Python

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, dire…

• UpdatedJul 12, 2020
• HTML

Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis" athttps://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analys…

• UpdatedDec 19, 2022
• C

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).

• UpdatedSep 4, 2024
• Roff

GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Described in the ASPLOS 2022 paper by Mansouri Ghiasi et al. athttps://people.inf.ethz.ch/omutlu/pub/GenS…

• UpdatedApr 6, 2022
• C

A scalable variant calling and benchmarking framework supporting both short and long reads.

• UpdatedOct 30, 2024
• Perl

GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.

• UpdatedOct 3, 2023
• C

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al.https…

• UpdatedJun 14, 2022

Space-efficient minimizer-based pangenome reference graph and haplotype mapping tool

• UpdatedMar 15, 2024
• Rust

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. athttps://arxiv.…

• UpdatedJul 7, 2021
• Jupyter Notebook

Highly optimized genomic resources for GPUs

• UpdatedSep 23, 2018
• C

Dynamic Mapping Simulator.

• UpdatedNov 19, 2016
• HTML

subset and spaced seed design tool

• UpdatedMay 2, 2024
• C++

SequenceLab is a benchmark suite for evaluating computational methods for comparing genomic sequences, such as pre-alignment filters and pairwise sequence alignment algorithms. SequenceLab is described by Rumpf et al. athttps://arxiv.org/abs/2310.16908

• UpdatedDec 23, 2023
• C++

coding problems from course 6 of the Bioinformatics specialization

• UpdatedJun 17, 2020
• Python

Reference-based read-mapper which performs ungapped alignment of sample reads on reference sequence.

• UpdatedDec 4, 2021
• Java

Illumina (and SOLiD) sensitive read mapping tool (cloned from svn://scm.gforge.inria.fr/svnroot/storm/, original code from@marta- , with some work done by@yoann-dufresne)

• UpdatedNov 16, 2017
• C