broadinstitute/long-read-pipelines

Long read production pipelines

Language: Jupyter Notebook - Size: 179 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 111 - Forks: 22

HKU-BAL/Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Language: Python - Size: 3.2 MB - Last synced: about 10 hours ago - Pushed: about 23 hours ago - Stars: 220 - Forks: 26

Nextomics/NextDenovo

Fast and accurate de novo assembler for long reads

Language: C - Size: 13.7 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 339 - Forks: 52

MeHelmy/princess

Language: Python - Size: 1.5 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 79 - Forks: 9

nf-core/taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Language: Nextflow - Size: 11.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 92 - Forks: 30

HKU-BAL/ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

Language: Python - Size: 3.46 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 51 - Forks: 5

bcgsc/ntLink

Minimizer-based assembly scaffolding and mapping using long reads

Language: Python - Size: 12.3 MB - Last synced: 15 days ago - Pushed: about 2 months ago - Stars: 27 - Forks: 7

bcgsc/LINKS

⛓ Long Interval Nucleotide K-mer Scaffolder

Language: Perl - Size: 28.8 MB - Last synced: 15 days ago - Pushed: 5 months ago - Stars: 70 - Forks: 15

HKU-BAL/ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Language: Python - Size: 1.93 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 29 - Forks: 2

MafaldaSFerreira/Atlherr_inversion_evol

Evolutionary genomics of chromosomal inversions in Atlantic herring

Language: R - Size: 639 KB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0

bsaintjo/cawlr-rs

Tool to analyze chromatin accessibility with long read sequencing technologies

Language: Jupyter Notebook - Size: 209 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 0 - Forks: 1

yangao07/abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Language: C - Size: 25.7 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 105 - Forks: 18

nanoporetech/pipeline-structural-variation 📦

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Language: Python - Size: 6.22 MB - Last synced: 7 days ago - Pushed: over 2 years ago - Stars: 110 - Forks: 16

at-cg/RAFT

Language: C++ - Size: 223 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 1

HKU-BAL/Clair3-Trio

Clair3-Trio: variant calling in trio using Nanopore long-reads

Language: Python - Size: 2.74 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 1

GoekeLab/sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Language: Jupyter Notebook - Size: 2.36 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 87 - Forks: 23

katerinakazantseva/stRainy

Graph-based assembly phasing

Language: Python - Size: 16.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 40 - Forks: 5

kishwarshafin/pepper

PEPPER-Margin-DeepVariant

Language: Python - Size: 36.1 MB - Last synced: 13 days ago - Pushed: 4 months ago - Stars: 231 - Forks: 41

bcgsc/straglr

Tandem repeat expansion detection or genotyping from long-read alignments

Language: Python - Size: 787 KB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 40 - Forks: 8

treangenlab/lemur

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

Language: Python - Size: 93.8 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

nf-core/detaxizer

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

Language: Nextflow - Size: 4.16 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 9 - Forks: 3

Yedomon/Benchmarking-long-reads-assemblers-for-Fusarium-oxysporum-genus-genome-assembly

Benchmarking for long-reads assembler

Size: 168 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 5 - Forks: 0

davidlougheed/strkit

A short tandem repeat (STR) genotyping and analysis toolkit for long reads

Language: Python - Size: 4.46 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 2 - Forks: 0

tobiasrausch/lorax

A long-read analysis toolbox for cancer and population genomics

Language: C++ - Size: 170 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 18 - Forks: 1

Xinglab/abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Language: C - Size: 26 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 12 - Forks: 3

lpryszcz/pyScaf

Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.

Language: Python - Size: 3.07 MB - Last synced: 25 days ago - Pushed: over 5 years ago - Stars: 24 - Forks: 11

SandraLouise/SVJedi-graph

SV genotyper for long reads with a variation graph

Language: Python - Size: 11.8 MB - Last synced: 2 months ago - Pushed: 8 months ago - Stars: 8 - Forks: 0

mortazavilab/lapa

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

Language: Jupyter Notebook - Size: 342 MB - Last synced: 15 days ago - Pushed: 6 months ago - Stars: 22 - Forks: 12

a-ludi/dentist

Close assembly gaps using long-reads at high accuracy.

Language: D - Size: 19.5 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 45 - Forks: 6

refresh-bio/colord

A versatile compressor of third generation sequencing reads.

Language: C++ - Size: 5.53 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 45 - Forks: 10

at-cg/minichain

Long-read aligner to pangenome graphs

Language: C - Size: 285 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 18 - Forks: 2

morispi/CONSENT

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Language: C++ - Size: 15.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 53 - Forks: 4

bioinfologics/Pseudoseq.jl

Fake genomes, fake sequencing, real insights.

Language: Julia - Size: 7.25 MB - Last synced: about 22 hours ago - Pushed: over 2 years ago - Stars: 13 - Forks: 3

natir/yacrd

Yet Another Chimeric Read Detector

Language: Rust - Size: 36.6 MB - Last synced: 21 days ago - Pushed: almost 2 years ago - Stars: 68 - Forks: 8

muellan/metacache

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

Language: C++ - Size: 149 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 55 - Forks: 10

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: 19 days ago - Pushed: 8 months ago - Stars: 5 - Forks: 0

Xinglab/TideHunter

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

Language: C - Size: 48.8 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 17 - Forks: 2

RajLabMSSM/isoseq-pipeline

pipeline for working with PacBio long read RNA data using the outputs of isoseq3

Language: Python - Size: 2.19 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 4

quadram-institute-bioscience/socru

Order and orientation of complete bacterial genomes

Language: Python - Size: 226 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 23 - Forks: 6

ksahlin/IsoCon

Derives consensus sequences from a set of long noisy reads by clustering and error correction.

Language: Python - Size: 1.15 MB - Last synced: 17 days ago - Pushed: almost 3 years ago - Stars: 13 - Forks: 1

andrewjpage/tiptoft

Predict plasmids from uncorrected long read data

Language: Python - Size: 37.8 MB - Last synced: 18 days ago - Pushed: over 4 years ago - Stars: 37 - Forks: 10

LankyCyril/edgecase

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Language: Python - Size: 167 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 14 - Forks: 2

GoekeLab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Language: R - Size: 637 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 118 - Forks: 19

algbio/GraphChainer

An accurate aligner of long reads to a variation graph, based on co-linear chaining

Language: C++ - Size: 305 KB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 25 - Forks: 3

yangao07/TideHunter

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

Language: C - Size: 48.9 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 22 - Forks: 5

shelkmike/Elloreas

Elloreas, a genome assembler

Language: Perl - Size: 915 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

seryrzu/centroFlye 📦

An algorithm for centromere assembly using long error-prone reads

Language: Python - Size: 4.82 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 25 - Forks: 5

morispi/HG-CoLoR

Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads

Language: C++ - Size: 7.61 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 9 - Forks: 3

anuradhawick/MetaBCC-LR

Reference-free Binning of Metagenomics Long Reads using Coverage and Composition

Language: Python - Size: 440 KB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 18 - Forks: 0

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

Language: HTML - Size: 148 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 27 - Forks: 7

vpc-ccg/haslr

A fast tool for hybrid genome assembly of long and short reads

Language: C++ - Size: 155 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 73 - Forks: 9

fabio-cunial/population-sv-simulator

Studies structural variant callers on large simulated populations sequenced with PacBio CCS

Language: C++ - Size: 9.44 MB - Last synced: 8 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

ganlab/GALA

Long-reads Gap-free Chromosome-scale Assembler

Language: Python - Size: 4.87 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 60 - Forks: 12

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: 19 days ago - Pushed: about 1 year ago - Stars: 46 - Forks: 10

djfeistel/SEWAGE

Synthetically Engineered Wastewater sequence data for Assessing Genomic Entities

Language: Python - Size: 535 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

natir/rustyread

A long read simulator based on badread idea

Language: Jupyter Notebook - Size: 6.34 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 21 - Forks: 2

natir/knot

KNOT: Knowledge Network Overlap exTraction is a tool for the investigation of fragmented long read assemblies.

Language: HTML - Size: 295 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

Nimauric/Mapler

A metagenome assembly and evaluation pipeline, focused on hi-fi long reads, but with support for lo-fi long reads and hybrid assemblies

Language: Python - Size: 236 KB - Last synced: 5 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

merlyescalona/yagcloser

YAGCloser: Yet-Another-Gap-Closer based on spanning of long reads.

Language: Python - Size: 85 KB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0

icemduru/HiFiAdapterTrimmer

Adapter+Barcode trimming from Pacbio HiFi reads

Language: Python - Size: 13.7 KB - Last synced: 4 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 1

GoekeLab/NanoporeRNASeq

Nanopore RNASeq data

Language: R - Size: 107 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - 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: 19 days ago - Pushed: about 2 years ago - Stars: 12 - Forks: 0

mariachiaragrieco/prunus-cp-genome-assembly

Assembly of chloroplast genome using long-reads and short-reads for Genomics Course 2021 (MSc Bioinformatics for Computational Genomics)

Language: Shell - Size: 10.7 KB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

ptrebert/project-diploid-assembly

Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data

Language: Jupyter Notebook - Size: 10.9 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 14 - Forks: 3

a-ludi/dentist-example 📦

A small example to test DENTIST's workflow

Language: Python - Size: 127 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

fritzsedlazeck/SVCollector

Method to optimally select samples for validation and resequencing

Language: C++ - Size: 1.98 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 23 - Forks: 5

TimD1/nPoRe

nPoRe: n-Polymer Realigner for improved pileup-based variant calling

Language: Python - Size: 493 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 12 - Forks: 0

smehringer/SViper

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

Language: C++ - Size: 6.65 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 30 - Forks: 8

gsiekaniec/ORI

ORI (Oxford nanopore Reads Identification) is a software allowing, from long nanopore reads, to identify the bacterial strains present in a sample.

Language: C++ - Size: 13.7 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

yjx1217/Varathon

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

Language: Perl - Size: 934 KB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 10 - Forks: 3

Magdoll/CoSA

Coronavirus (SARS-Cov-2) sequencing analysis

Language: Python - Size: 2.85 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 10 - Forks: 6

wtsi-hpag/smis Fork of fg6/smis

SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)

Language: C - Size: 42.1 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 3 - Forks: 1

seryrzu/centroFlye_paper_scripts

Scripts for the Nature Biotechnology paper, 2020: Automated assembly of centromeres from ultra-long error-prone reads

Language: Jupyter Notebook - Size: 2.81 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

AustralianBioCommons/Canu

Canu: structured documentation and results of testing / optimisation for Australian compute infrastructures

Size: 139 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 1

AustralianBioCommons/falcon

Language: Python - Size: 147 KB - Last synced: 11 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 3

vmurigneu/micropipe_pawsey

Documentation for running microPIPE at Pawsey

Size: 2.25 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

AustralianBioCommons/ipa

Improved Phased Assembler: structured documentation and results of testing for Australian compute infrastructures

Size: 27.3 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 2

hitbc/TideHunter

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

Language: C - Size: 435 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

xjtu-omics/Scissor

A flexible complex genome rearrangement simulator for short and long reads

Language: Python - Size: 117 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0