Topic: "sequence-alignment"
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
Language: Python - Size: 70.7 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 4,849 - Forks: 1,853
lh3/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Language: C - Size: 1.62 MB - Last synced at: 22 days ago - Pushed at: 3 months ago - Stars: 2,089 - Forks: 447
lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Language: C - Size: 1.7 MB - Last synced at: 22 days ago - Pushed at: 9 months ago - Stars: 1,681 - Forks: 567
bbuchfink/diamond
Accelerated BLAST compatible local sequence aligner.
Language: C++ - Size: 32.2 MB - Last synced at: 9 days ago - Pushed at: 11 days ago - Stars: 1,219 - Forks: 185
bwa-mem2/bwa-mem2
The next version of bwa-mem
Language: C++ - Size: 2.61 MB - Last synced at: 25 days ago - Pushed at: 3 months ago - Stars: 798 - Forks: 116
torognes/vsearch
Versatile open-source tool for microbiome analysis
Language: C++ - Size: 7.06 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 728 - Forks: 130
biojava/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Language: Java - Size: 48.9 MB - Last synced at: 3 days ago - Pushed at: 12 days ago - Stars: 619 - Forks: 397
Martinsos/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
Language: C++ - Size: 4.67 MB - Last synced at: 25 days ago - Pushed at: 8 months ago - Stars: 571 - Forks: 174
lh3/minigraph
Sequence-to-graph mapper and graph generator
Language: C - Size: 896 KB - Last synced at: 22 days ago - Pushed at: 5 months ago - Stars: 464 - Forks: 40
seqan/seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Language: C++ - Size: 22.5 MB - Last synced at: 12 days ago - Pushed at: 16 days ago - Stars: 444 - Forks: 87
lh3/miniprot
Align proteins to genomes with splicing and frameshift
Language: C - Size: 361 KB - Last synced at: 22 days ago - Pushed at: 3 months ago - Stars: 388 - Forks: 21
microsoft/bistring
Bidirectionally transformed strings
Language: Python - Size: 978 KB - Last synced at: 5 days ago - Pushed at: almost 2 years ago - Stars: 370 - Forks: 16
wurmlab/sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Language: JavaScript - Size: 121 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 289 - Forks: 117
shenwei356/LexicMap
LexicMap: efficient sequence alignment against millions of prokaryotic genomes
Language: Go - Size: 42.7 MB - Last synced at: 10 days ago - Pushed at: 13 days ago - Stars: 204 - Forks: 8
moshi4/pyMSAviz
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Language: Python - Size: 7.2 MB - Last synced at: 25 days ago - Pushed at: about 1 year ago - Stars: 168 - Forks: 20
TimoLassmann/kalign
A fast multiple sequence alignment program.
Language: C - Size: 1.81 MB - Last synced at: 27 days ago - Pushed at: 6 months ago - Stars: 149 - Forks: 30
lh3/ksw2
Global alignment and alignment extension
Language: C - Size: 189 KB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 134 - Forks: 27
cogent3/cogent3
Comparative Genomics Toolkit 3
Language: Python - Size: 47.1 MB - Last synced at: about 4 hours ago - Pushed at: 3 days ago - Stars: 133 - Forks: 65
flatironinstitute/deepblast
Neural Networks for Protein Sequence Alignment
Language: Python - Size: 56.7 MB - Last synced at: 6 months ago - Pushed at: about 1 year ago - Stars: 123 - Forks: 22
jguhlin/minimap2-rs
Rust bindings to minimap2 library
Language: Jupyter Notebook - Size: 23.7 MB - Last synced at: 7 days ago - Pushed at: 17 days ago - Stars: 102 - Forks: 18
drostlab/orthologr
Genome wide orthology inference and dNdS estimation
Language: R - Size: 103 MB - Last synced at: 12 days ago - Pushed at: 4 months ago - Stars: 96 - Forks: 30
CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Language: TypeScript - Size: 254 MB - Last synced at: 23 days ago - Pushed at: 26 days ago - Stars: 95 - Forks: 42
lh3/unimap
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
Language: C - Size: 487 KB - Last synced at: 8 months ago - Pushed at: over 4 years ago - Stars: 88 - Forks: 4
kensho-technologies/sequence_align
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
Language: Python - Size: 201 KB - Last synced at: 4 months ago - Pushed at: 10 months ago - Stars: 73 - Forks: 3
RWilton/Arioc
Arioc: GPU-accelerated DNA short-read alignment
Size: 16.9 MB - Last synced at: 23 days ago - Pushed at: 8 months ago - Stars: 70 - Forks: 8
biocommons/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Language: Python - Size: 14.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 65 - Forks: 24
zhou-lab/biscuit
BISulfite-seq CUI Toolkit
Language: C - Size: 6.79 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 64 - Forks: 24
BioJulia/BioAlignments.jl
Sequence alignment tools
Language: Julia - Size: 1.1 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 64 - Forks: 24
CMU-SAFARI/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.
Language: VHDL - Size: 21.2 MB - Last synced at: 23 days ago - Pushed at: almost 3 years ago - Stars: 53 - Forks: 11
rdpstaff/RDPTools
Collection of commonly used RDP Tools for easy building
Language: Makefile - Size: 37.1 KB - Last synced at: 25 days ago - Pushed at: over 2 years ago - Stars: 51 - Forks: 53
lh3/miniwfa
A reimplementation of the WaveFront Alignment algorithm at low memory
Language: C - Size: 197 KB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 49 - Forks: 4
ITBE-Lab/MA
The Modular Aligner and The Modular SV Caller
Language: C++ - Size: 11.4 MB - Last synced at: 24 days ago - Pushed at: over 2 years ago - Stars: 46 - Forks: 3
estebanpw/chromeister
A dotplot generator for large chromosomes
Language: C - Size: 927 KB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 43 - Forks: 5
Martinsos/opal
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
Language: C++ - Size: 19 MB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 39 - Forks: 10
lh3/bioseq-js
For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml
Language: HTML - Size: 16.6 KB - Last synced at: 19 days ago - Pushed at: over 6 years ago - Stars: 39 - Forks: 16
althonos/pyfamsa
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
Language: Cython - Size: 273 KB - Last synced at: 25 days ago - Pushed at: 29 days ago - Stars: 36 - Forks: 3
nahmedraja/GASAL2
Language: C++ - Size: 8.82 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 36 - Forks: 11
brianli314/palindrome-finder
A bioinformatics tool written in Rust to find palindromic sequences in DNA
Language: Rust - Size: 149 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 35 - Forks: 1
quim0/WFA-GPU
GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
Language: C - Size: 5 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 35 - Forks: 3
arshajii/ema
Fast & accurate alignment of barcoded short-reads
Language: C++ - Size: 252 KB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 6
thekaplanlab/msabrowser
🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations
Language: JavaScript - Size: 412 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 31 - Forks: 7
sanderlab/alignmentviewer
Multiple sequence alignment visualizer
Language: JavaScript - Size: 9.26 MB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 30 - Forks: 6
datasnakes/OrthoEvolution
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
Language: Python - Size: 41.3 MB - Last synced at: 27 days ago - Pushed at: 29 days ago - Stars: 28 - Forks: 4
baku4/sigalign
A Similarity-Guided Alignment Algorithm
Language: Rust - Size: 11.7 MB - Last synced at: 3 days ago - Pushed at: 7 months ago - Stars: 28 - Forks: 4
Nazeeefa/awesome-sequencing-tech
A collection of publications on comparison of high-throughput sequencing technologies.
Size: 219 KB - Last synced at: 26 days ago - Pushed at: 29 days ago - Stars: 27 - Forks: 3
lorenzocestaro/seqalign
Collection of sequence alignment algorithms.
Language: JavaScript - Size: 366 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 25 - Forks: 3
ropensci/phylotaR
An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
Language: R - Size: 15.2 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 24 - Forks: 9
ppillot/biomsalign
JavaScript library for Multiple Sequence Alignment
Language: TypeScript - Size: 622 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 0
althonos/pymuscle5
Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
Language: Cython - Size: 115 KB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 2
benhid/pyMSA
Scoring multiple sequence alignments with Python
Language: Python - Size: 1.34 MB - Last synced at: 17 days ago - Pushed at: over 2 years ago - Stars: 23 - Forks: 10
trishume/seqalign_pathing
Rust implementation of sequence alignment / Levenshtein distance by A* acceleration of the DP algorithm
Language: Rust - Size: 5.86 KB - Last synced at: 3 months ago - Pushed at: over 8 years ago - Stars: 22 - Forks: 3
ranwez/MACSE_V2_PIPELINES
This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.
Language: Shell - Size: 4 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 21 - Forks: 8
IbrahimTanyalcin/lexicon-mono-seq
DOM Text Based Multiple Sequence Alignment Library
Language: JavaScript - Size: 117 MB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 20 - Forks: 5
safaad/aim
AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.org/10.1093/bioinformatics/btad155
Language: C - Size: 1.18 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 19 - Forks: 2
robinvanderlee/positive-selection
Scripts and procedures for detecting positively selected genes and codons in primates
Language: Perl - Size: 169 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 19 - Forks: 16
laurentnoe/yass
genomic alignment similarity search tool
Language: C - Size: 515 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 18 - Forks: 6
CaoTianze/plotnineseqsuite
plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style
Language: Python - Size: 11 MB - Last synced at: 10 days ago - Pushed at: 13 days ago - Stars: 17 - Forks: 0
algbio/emerald
EMERALD calculates safety-windows by exploring the suboptimal alignment space
Language: C++ - Size: 1.35 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 17 - Forks: 0
LKremer/MSA_trimmer
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
Language: Python - Size: 8.79 KB - Last synced at: 6 months ago - Pushed at: almost 7 years ago - Stars: 17 - Forks: 2
jasonlin316/Systolic-Array-for-Smith-Waterman
This work implements a dynamic programming algorithm for performing local sequence alignment. Through parallelism, it can run 136X times faster than a software running the same algorithm.
Language: Verilog - Size: 12.4 MB - Last synced at: almost 3 years ago - Pushed at: over 6 years ago - Stars: 16 - Forks: 6
tmaklin/kbo
Local alignment search with k-bounded matching statistics.
Language: Rust - Size: 350 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 15 - Forks: 2
gata-bio/faster-fasta
Faster FASTA file processing command line tool - parsing, sorting, deduplication, transliteration, and reverse complements
Language: Rust - Size: 43 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 14 - Forks: 1
aziele/pairwise-sequence-alignment
A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water
Language: Python - Size: 44.9 KB - Last synced at: 3 months ago - Pushed at: 10 months ago - Stars: 14 - Forks: 3
brentp/spacepile
convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.
Language: Rust - Size: 31.3 KB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 0
NAL-i5K/genomics-workspace
Django website project for common sequence search tools.
Language: JavaScript - Size: 444 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 14 - Forks: 5
lignum-vitae/goombay
Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.
Language: Python - Size: 467 KB - Last synced at: 15 days ago - Pushed at: 3 months ago - Stars: 13 - Forks: 3
iosonofabio/seqanpy
Fast pairwise sequence alignment using SeqAn, in Python.
Language: C++ - Size: 32.2 KB - Last synced at: 3 months ago - Pushed at: almost 7 years ago - Stars: 13 - Forks: 7
mmtechslv/nwunch
Implementation of Needleman-Wunsch algorithm in Python Using Nested Functions.
Language: Python - Size: 1.95 KB - Last synced at: almost 3 years ago - Pushed at: over 7 years ago - Stars: 13 - Forks: 4
broadinstitute/g2papi
Python Client Library for the G2P Portal API
Language: Python - Size: 4.35 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 2
AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Language: HTML - Size: 68.5 MB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 42
mhahsler/rMSA
Interface to Popular Multiple Sequence Alignment Tools - R-package
Language: TeX - Size: 613 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 1
CMU-SAFARI/GenStore
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. at https://people.inf.ethz.ch/omutlu/pub/GenStore_asplos22-arxiv.pdf
Language: C - Size: 2.26 MB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 12 - Forks: 0
chchch/sanskrit-alignment
Sequence alignment and textual reconstruction for Sanskrit texts
Language: JavaScript - Size: 45.4 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 11 - Forks: 3
CMU-SAFARI/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).
Language: Roff - Size: 63 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 4
jia-zhuang/mapper
Short reads aligner for NIPT/CNV
Language: C - Size: 34.2 KB - Last synced at: almost 3 years ago - Pushed at: about 7 years ago - Stars: 11 - Forks: 5
btmartin721/raxml_ascbias
Script for removing or counting invariant sites for the RAxML ascertainment bias corrections
Language: Python - Size: 25.4 KB - Last synced at: almost 3 years ago - Pushed at: over 7 years ago - Stars: 11 - Forks: 1
unum-bio/AffineGaps
Less-wrong single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman–Wunsch, Smith-Waterman, and Levenshtein algorithms for sequence alignment
Language: Python - Size: 149 KB - Last synced at: 10 days ago - Pushed at: 2 months ago - Stars: 10 - Forks: 0
althonos/pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
Language: Cython - Size: 301 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 10 - Forks: 1
Jong-hun-Park/trviz
A python library for decomposing and visualizing tandem repeat sequences
Language: Python - Size: 2.64 MB - Last synced at: 24 days ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 1
s-andrews/redotable
A dotplot application for DNA/RNA sequence
Language: Java - Size: 388 KB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 1
SanojPunchihewa/f5n
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
Language: Java - Size: 123 MB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 7
AshokHub/locBLAST
Local NCBI BLAST+ Search
Language: PHP - Size: 42.4 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 10 - Forks: 8
chasewnelson/EBT
Evolutionary Bioinformatics Toolkit (EBT)
Language: Perl - Size: 99.6 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 10 - Forks: 4
KVD-lab/puma
Papillomavirus genome annotation tool
Language: Python - Size: 13.4 MB - Last synced at: 24 days ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 3
Gagniuc/Visual-Sequence-Alignment-in-VB6
This highly visual and responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time.
Language: Visual Basic 6.0 - Size: 7.26 MB - Last synced at: 10 months ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 2
lh3/editdist-U85
Fast implementation of Ukkenon's O(ND) algorithm for computing edit distance
Language: C - Size: 25.4 KB - Last synced at: 8 months ago - Pushed at: over 3 years ago - Stars: 9 - Forks: 1
poke1024/vectorian-legacy 📦
A search engine for intertextual references based on sequence alignments of word embeddings
Language: JavaScript - Size: 934 KB - Last synced at: almost 3 years ago - Pushed at: almost 5 years ago - Stars: 9 - Forks: 1
Serafim-End/periodicity-research
The research of accuracy of searching cycles methods in symbolic sequences (time series) with presence of random noises.
Language: Python - Size: 2.68 MB - Last synced at: almost 3 years ago - Pushed at: about 6 years ago - Stars: 9 - Forks: 2
TravisWheelerLab/polyA
Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)
Language: Python - Size: 59 MB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 2
caioss/miga
MIGA is a Python package that provides a GPU-accelerated MSA-based mutual information optimizer
Language: Python - Size: 295 KB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 2
CMU-SAFARI/Molecules2Variations
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://arxiv.org/abs/2205.07957
Size: 4.31 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 0
rmtheis/mummergpu 📦
Fork of MUMmerGPU-2.0 that compiles without errors
Language: C++ - Size: 66.4 KB - Last synced at: almost 3 years ago - Pushed at: over 8 years ago - Stars: 8 - Forks: 4
MikePodsytnik/TCRtrie
Fast trie-based search for TCR sequences with Levenshtein and substitution matrix support
Language: C++ - Size: 1.1 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 7 - Forks: 1
hallamlab/samsum
A light-weight python package for summarizing sequence coverage from SAM and BAM files
Language: Python - Size: 1.92 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 3
gaojunxuan/chrom_mini_graph
Space-efficient minimizer-based pangenome reference graph and haplotype mapping tool
Language: Rust - Size: 32.5 MB - Last synced at: 8 months ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 0
drostlab/rdiamond
Running DIAMOND2 through R
Language: R - Size: 628 KB - Last synced at: 6 months ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 2
CMU-SAFARI/GateSeeder
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.
Language: C - Size: 1.24 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 0
lorenzocestaro/graphic-smith-waterman 📦
Javascript implementation of the Smith-Waterman algorithm for sequence alignment.
Language: JavaScript - Size: 800 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 1
nanxstats/ssw-r
🚀 R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD
Language: R - Size: 1.36 MB - Last synced at: 23 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0
biocommons/uta-align
C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.
Language: Cython - Size: 350 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 5