long-reads

There are 6 repositories under long-reads topic.

Nextomics / NextDenovo
Fast and accurate de novo assembler for long reads
assembler genome-assembly long-reads oxford-nanopore pacbio
Language:C 395
HKU-BAL / Clair3
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
computational-biology deep-learning genomics illumina long-reads nanopore ont-data ont-models pacbio variant-calling variant-detection
Language:Python 299
kishwarshafin / pepper
PEPPER-Margin-DeepVariant
nanopore long-reads oxford-nanopore variant-calling genome-variation assembly-polishing pacbio-ccs variants
Language:Python 247
bambu
GoekeLab / bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
bambu transcript-reconstruction transcript-quantification long-reads nanopore-sequencing transcriptomics rna-seq-analysis bioconductor r nanopore rna-seq
Language:R 217
nf-core / taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
metagenomics profiling taxonomic-profiling shotgun nf-core nextflow workflow pipeline classification microbiome taxonomic-classification long-reads nanopore bioinformatics illumina pathogen
Language:Nextflow 161
broadinstitute / long-read-pipelines
Long read production pipelines
pipelines wdl long-reads de-novo-assembly variant-calling
Language:Jupyter Notebook 148
sg-nex-data
GoekeLab / sg-nex-data
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
nanopore rna-seq direct-rna-sequencing long-reads transcriptomics
Language:R 135
bcgsc / straglr
Tandem repeat expansion detection or genotyping from long-read alignments
bioinformatics genomics long-reads tandem-repeats
Language:Python 124
yangao07 / abPOA
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
alignment-graph banded-dp consensus-sequence consensus-sequences gfa-format long-reads multiple-sequence-alignment partial-order-alignment simd
Language:C 119
nanoporetech / pipeline-structural-variation
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
nanopore structural-variation whole-genome-sequencing long-reads
Language:Python 114
katerinakazantseva / strainy
Graph-based assembly phasing
assembly hifi long-read-sequencing long-reads metagenomic-analysis metagenomics nanopore sequencing
Language:Python 87
HKU-BAL / ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
bioinformatics deep-learning genomics haplotypes illumina indels long-read-sequencing long-reads nanopore ont pacbio phasing short-reads snvs somatic-mutations somatic-variants
Language:Python 82
natir / yacrd
Yet Another Chimeric Read Detector
bioinformatics chimera long-reads sequence
Language:Rust 80
ganlab / GALA
Long-reads Gap-free Chromosome-scale Assembler
pacbio nanopore genome-assembly genome-analysis scaffolding long-reads gap-filling
Language:Python 79
MeHelmy / princess
long-reads structural-variation single-nucleotide-variation methylation phasing
Language:Python 79
vpc-ccg / haslr
A fast tool for hybrid genome assembly of long and short reads
bioinformatics genomics genome-assembly hybrid-assembly long-reads pacbio nanopore
Language:C++ 77
bcgsc / LINKS
⛓ Long Interval Nucleotide K-mer Scaffolder
bloom-filter draft-assembly extract-kmer-pairs genome-assemblies long-reads scaffold scaffold-layout
Language:Perl 74
muellan / metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq fasta fastq dna-sequences genomic-data-analysis classification bioinformatics bioinformatics-tool bioinformatics-algorithms short-read-mapper long-reads
Language:C++ 64
HKU-BAL / ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning genomics illumina long-read-sequencing long-reads nanopore ont pacbio snvs somatic-mutations somatic-variants tumor-only tumors variant-calling variants
Language:Python 59
morispi / CONSENT
Scalable long read self-correction and assembly polishing with multiple sequence alignment
ngs correction long-reads long reads self-correction self msa multiple-sequence-alignment consensus contigs assembly polishing
Language:C++ 55
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.
sequence-aligner fpga gpu hardware-accelerator minimap2 edlib smith-waterman needleman-wunsch pre-alignment-filtering sequence-alignment long-reads short-reads wavefront-alignment
Language:VHDL 52
refresh-bio / colord
A versatile compressor of third generation sequencing reads.
bioinformatics compression fastq-files genomics long-reads oxford-nanopore pac-bio sequencing
Language:C++ 50
dentist
a-ludi / dentist
Close assembly gaps using long-reads at high accuracy.
genome-assembly gap-filling pacbio long-reads close-assembly-gaps snakemake damapper cluster daligner dub singularity docker bioinformatics
Language:D 48
andrewjpage / tiptoft
Predict plasmids from uncorrected long read data
genomics oxford-nanopore nanopore plasmid pacbio uncorrected research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen long-reads kmer plasmidfinder
Language:Python 39
bcgsc / ntLink
Minimizer-based assembly scaffolding and mapping using long reads
assembly bioinformatics long-reads minimizers scaffolding
Language:Python 37
orangeSi / GSSplayground
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, directly modify almost all features in Chrome by click the feature
genomes genecluster synteny crosslink bioinformatics svg vcf snp bam read-mapping depth visualization structure-variation genome-viewer sv transcriptomics igv-like comparative-genomics long-reads indel
Language:HTML 33
algbio / GraphChainer
An accurate aligner of long reads to a variation graph, based on co-linear chaining
long-reads pangenomics read-aligners variation-graph
Language:C++ 32
smehringer / SViper
Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
genetics decode-genetics long-reads correction structural-variation seqan
Language:C++ 32
mortazavilab / lapa
Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
bioinformatics long-reads polyadenylation rna-seq transcription
Language:Jupyter Notebook 29
yangao07 / TideHunter
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
long-reads seed-and-chain multiple-sequence-alignment partial-order-alignment tandem-repeats
Language:C 29
fritzsedlazeck / SVCollector
Method to optimally select samples for validation and resequencing
ngstools ngs bioinformatics structural-variation vcf long-reads
Language:C++ 27
quadram-institute-bioscience / socru
Order and orientation of complete bacterial genomes
bioinformatics python3 bacteria long-reads assembly complete bioinformatics-pipeline infectious-diseases genomics
Language:Python 27
at-cg / minichain
Long-read aligner to pangenome graphs
alignment long-reads pangenomics
Language:C 26
seryrzu / centroFlye
An algorithm for centromere assembly using long error-prone reads
genome-assembly genomics long-reads long-read-sequencing centromere
Language:Python 26
lpryszcz / pyScaf
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
genome long-reads reference scaffolding synteny
Language:Python 24
treangenlab / lemur
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
long-read-sequencing long-reads metagenomic-analysis metagenomic-classification metagenomics taxonomic-classification taxonomic-profiling
Language:Python 23