Fast and accurate de novo assembler for long reads
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May 10, 2024 - C
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long-reads
Here are 92 public repositories matching this topic...
Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling
deep-learning nanopore genomics computational-biology pacbio variant-calling illumina long-reads variant-detection ont-data ont-models
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Feb 26, 2026 - Python
PEPPER-Margin-DeepVariant
nanopore variants variant-calling oxford-nanopore genome-variation long-reads pacbio-ccs assembly-polishing
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Jan 12, 2024 - Python
Reference-guided transcript discovery and quantification for long read RNA-Seq data
rna-seq r nanopore bioconductor transcriptomics rna-seq-analysis transcript-quantification bambu long-reads nanopore-sequencing transcript-reconstruction
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Feb 20, 2026 - R
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling microbiome illumina long-reads taxonomic-classification nf-core taxonomic-profiling
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Feb 28, 2026 - Nextflow
Long read production pipelines
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Feb 26, 2026 - Jupyter Notebook
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
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Jan 23, 2026 - R
Tandem repeat expansion detection or genotyping from long-read alignments
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Nov 24, 2025 - Python
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
simd long-reads multiple-sequence-alignment partial-order-alignment consensus-sequences banded-dp consensus-sequence alignment-graph gfa-format
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Feb 22, 2026 - C
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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Oct 25, 2021 - Python
ClairS - a deep-learning method for long-read somatic small variant calling
bioinformatics deep-learning nanopore genomics somatic-variants haplotypes pacbio somatic-mutations illumina indels phasing snvs long-reads ont long-read-sequencing short-reads
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Jan 22, 2026 - Python
Graph-based assembly phasing
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Nov 25, 2025 - Python
Yet Another Chimeric Read Detector
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Nov 7, 2024 - Rust
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Mar 3, 2025 - Python
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning nanopore genomics somatic-variants variants pacbio variant-calling somatic-mutations illumina snvs long-reads ont long-read-sequencing tumors tumor-only
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Nov 13, 2025 - Python
Long-reads Gap-free Chromosome-scale Assembler
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Mar 21, 2023 - Python
A fast tool for hybrid genome assembly of long and short reads
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Apr 22, 2020 - C++
⛓ Long Interval Nucleotide K-mer Scaffolder
bloom-filter scaffold long-reads draft-assembly extract-kmer-pairs genome-assemblies scaffold-layout
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Apr 1, 2025 - Perl
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
bioinformatics genome taxonomy metagenomics classification fasta fastq metagenomes dna-sequences short-read-mapper read-mapping metagenomic-analysis metagenomic-classification genomic-data-analysis bioinformatics-algorithms long-reads metagenomic-data refseq ncbi-refseq bioinformatics-tool
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Jan 22, 2026 - C++
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.o…
fpga gpu smith-waterman needleman-wunsch sequence-alignment long-reads minimap2 short-reads hardware-accelerator sequence-aligner edlib pre-alignment-filtering wavefront-alignment
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Mar 31, 2023 - VHDL
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