LabShengLi/nanome

NANOME pipeline (Nanopore long-read sequencing consensus DNA methylation detection method and pipeline)

Language: Python - Size: 128 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 30 - Forks: 9

deepomicslab/SpecImmune

Accurate Typing of Diverse Immune-Related Gene Families from Long-Read Sequencing Data. It can handle HLA, KIR, IG, TCR, CYP gene families. It supports both WGS and amplicon data. It supports PacBio and Nanopore data.

Language: F* - Size: 595 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 23 - Forks: 0

akikuno/DAJIN2

🔬 Genotyping tool for genome-edited samples using nanopore-targeted sequencing

Language: Python - Size: 561 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 14 - Forks: 0

ACEnglish/kanpig

Kmer Analysis of Pileups for Genotyping

Language: Rust - Size: 5.05 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 30 - Forks: 3

barricklab/seabreeze Fork of ira-zibbu/seabreeze-ltee-analysis

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies

Language: Python - Size: 20 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 1

Xinglab/ProteoSeq

ProteoSeq: A proteogenomics workflow leveraging long-read RNA-seq data for discovery of isoform-level peptides and proteins.

Language: Python - Size: 71.8 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0

davidlougheed/strkit

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

Language: Python - Size: 5.04 MB - Last synced at: 1 day ago - Pushed at: 9 days ago - Stars: 13 - Forks: 1

Clinical-Genomics/stranger

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

Language: Python - Size: 484 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 32 - Forks: 6

genomic-medicine-sweden/nallo

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Language: Nextflow - Size: 100 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 32 - Forks: 10

huangnengCSU/longcallR

LongcallR is a SNP caller for single molecule long-read RNA-seq data

Language: Rust - Size: 19.2 MB - Last synced at: 9 days ago - Pushed at: 21 days ago - Stars: 62 - Forks: 4

Nirmal2310/ANOMALY

Snakemake workflow for calling NUMTs from Long read sequencing data. The pipeline takes either FASTQ or BAM file and outputs a text file containing NUMTs.

Language: Shell - Size: 5.53 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 3 - Forks: 0

quadram-institute-bioscience/galaxy-tools

A collection of bioinformatics tools for use with galaxy written at Quadram Institute

Language: HTML - Size: 326 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 4 - Forks: 3

aweich/VIS

Snakemake workflow for the detection of vector insertion sites (VIS) in long-read sequencing data

Language: Python - Size: 11.3 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 2 - Forks: 1

nf-core/mag

Assembly and binning of metagenomes

Language: Nextflow - Size: 37 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 239 - Forks: 132

Nazeeefa/awesome-sequencing-tech-papers

A collection of publications on comparison of high-throughput sequencing technologies.

Size: 173 KB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 28 - Forks: 3

michael-nakai/isopod

An R package to simulate and detect differential transcript usage in transcript-level single-cell datasets.

Language: R - Size: 608 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 6 - Forks: 0

nf-core/scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

Language: Nextflow - Size: 40.6 MB - Last synced at: 25 days ago - Pushed at: 26 days ago - Stars: 36 - Forks: 14

HKU-BAL/ClairS

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

Language: Python - Size: 12.7 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 84 - Forks: 8

bsaintjo/pod5-rs

Rust library to support interacting with Oxford Nanopore POD5 files

Language: Rust - Size: 2.87 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 5 - Forks: 1

Xinglab/scCirRL-seq

Haplotype-resolved full-length transcriptome analysis in single cells by scCirRL-seq

Language: Python - Size: 3.25 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

google/deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Language: Python - Size: 140 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 240 - Forks: 37

HudsonAlpha/fmlrc2

Language: Rust - Size: 168 KB - Last synced at: 25 days ago - Pushed at: over 2 years ago - Stars: 47 - Forks: 5

ylab-hi/DeepChopper

Language models identify chimeric artificial reads in NanoPore direct-RNA sequencing data.

Language: Rust - Size: 1.49 GB - Last synced at: 8 days ago - Pushed at: 20 days ago - Stars: 4 - Forks: 1

AstraBert/simON-reads

simON-reads ("Simulate Oxford Nanopore Reads") is a simple yet powerful tool to generate fastq files containing MiniON-like long reads

Language: Python - Size: 95.7 KB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

SalomonisLab/altanalyze3

AltAnalyze version 3 is a Python3 library to integrate and compare diverse RNA isoform datasets.

Language: Python - Size: 14 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 3

xinehc/argo

Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping

Language: Python - Size: 31.3 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 0

JensUweUlrich/Taxor

Fast and space-efficient taxonomic classification of long reads

Language: C++ - Size: 716 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 43 - Forks: 2

gaolabtools/scNanoGPS

Single cell Nanopore sequencing data for Genotype and Phenotype

Language: Python - Size: 27 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 51 - Forks: 5

katerinakazantseva/strainy

Graph-based assembly phasing

Language: Python - Size: 17.2 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 80 - Forks: 6

nf-core/viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

Language: Nextflow - Size: 9.89 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 137 - Forks: 128

xinehc/melon

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Language: Python - Size: 47.9 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 34 - Forks: 1

WhaleGe/jaffatools

A Python toolkit for JAFFA fusion gene detection

Language: Python - Size: 37.1 KB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0

baigal628/NEMO

a deep neural network model for mapping modifications in nanopore Long-read sequencing data

Language: Python - Size: 123 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 1

HKU-BAL/Clair3-RNA

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Language: Python - Size: 528 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 22 - Forks: 1

bcgsc/goldrush

Linear-time de novo Long Read Assembler

Language: C++ - Size: 4.26 MB - Last synced at: 28 days ago - Pushed at: 5 months ago - Stars: 40 - Forks: 2

Serka-M/mmlong2

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

Language: Python - Size: 2.71 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 45 - Forks: 5

josiegleeson/BamSlam

Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files

Language: R - Size: 125 KB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 5

tobiasrausch/lorax

A long-read analysis toolbox for cancer and population genomics

Language: C++ - Size: 203 KB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 22 - Forks: 1

nschan/nf-genomeassembly

Nextflow pipeline to assemble genomes from long reads.

Language: Nextflow - Size: 1000 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

HKU-BAL/ClairS-TO

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

Language: Python - Size: 9.89 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 59 - Forks: 4

monarch-initiative/SvAnna

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

Language: Java - Size: 3.72 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 36 - Forks: 4

dyxstat/MetaCC

MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

Language: C - Size: 13 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 8 - Forks: 2

treangenlab/lemur

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

Language: Python - Size: 58.6 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 24 - Forks: 1

Serka-M/mmlong2-lite

Lightweight bioinformatics pipeline for microbial genome recovery

Language: Python - Size: 1.18 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 9 - Forks: 3

jcaperella29/ISOVIZ_Shiny_APP

I have prepared a GUI for the new R package ISOVIZ using the Shiny web application framework. it is deployed at the url below.

Language: R - Size: 30.3 KB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

akikuno/midsv

a Python module to translate SAM into MIDSV format.

Language: Python - Size: 14.2 MB - Last synced at: 25 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

yanhui09/laca

A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)

Language: Python - Size: 124 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 7 - Forks: 2

tseemann/berokka

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Language: Perl - Size: 3.51 MB - Last synced at: 3 months ago - Pushed at: almost 6 years ago - Stars: 26 - Forks: 3

codecreatede/go-metagenomics-deep

golang complete metagenomics analysis long reads

Language: Go - Size: 1000 Bytes - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

ksahlin/ultra

Long-read splice alignment with high accuracy

Language: Python - Size: 2 GB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 59 - Forks: 10

ayoraind/tracm_nextflow

Nextflow pipeline incorporating the tracm/tracs alignment step alone.

Language: Nextflow - Size: 11.7 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

HYzhang800/CLN3_public_long_read

Codes for CLN3 public long-read RNA sequencing data analysis

Language: R - Size: 1.57 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

jasonwong-lab/smk_sv

A snakemake pipeline to call structure variants from ONT data

Language: Python - Size: 4.31 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0

lasseignelab/230227_EJ_MouseBrainIsoDiv

This repository is the current repository for our Jones et al. 2024 manuscript titled Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage.

Language: R - Size: 53.7 MB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

AstraBert/VirBiCla

A novel ML-based binary classifier to tell viral and non-viral long reads apart in metagenomic samples.

Language: Python - Size: 49.1 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

kaist-ina/RUN-DVC

Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning

Language: Python - Size: 3.5 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 0

LauraSkak/Modification-count-workflow

This workflow uses Dorado, Samtools, Clair3, WhatHap and Modkit to extract a modification count table containing information for each relevant site.

Language: Python - Size: 225 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

BeatsonLab-MicrobialGenomics/micropipe

A pipeline for high-quality bacterial genome construction using ONT sequencing

Language: HTML - Size: 57.4 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 36 - Forks: 9

HudsonAlpha/rust-fastleng

a fastx parser for generating sequence length metrics

Language: Rust - Size: 35.2 KB - Last synced at: 20 days ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 2

comprna/reorientexpress

Transcriptome long-read orientation with Deep Learning

Language: Python - Size: 114 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 4

seryrzu/centroFlye 📦

An algorithm for centromere assembly using long error-prone reads

Language: Python - Size: 4.82 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 25 - Forks: 5

noush-joglekar/scisorseqr

scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

Language: R - Size: 1010 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 26 - Forks: 7

collaborativebioinformatics/isocomp

Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq

Language: HTML - Size: 49 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 8

marithetland/ONTmompS

Get L. pneumophila ST from long-read or hybrid assemblies.

Language: Python - Size: 116 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

sanekun/HT-techniques-synbio

Additional data for matser_thesis in UST

Language: HTML - Size: 5.48 MB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

sheynkman-lab/Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

Language: Python - Size: 108 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 30 - Forks: 12

IGDRion/ANNEXseq

Nextflow pipeline to combine nanoseq and ANNEXA for long-read RNASeq data

Language: Nextflow - Size: 2.68 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

icemduru/HiFiAdapterTrimmer

Adapter+Barcode trimming from Pacbio HiFi reads

Language: Python - Size: 13.7 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

rx32940/Environmental_Lepto_detection

Comparing 3 different metagenomics approaches with ONT's long read sequencing method

Language: Shell - Size: 43 KB - Last synced at: 8 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

jiadong324/ComparStra-Parser

Scripts used to compare SVs detected from long read and long read assembly

Language: Python - Size: 134 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

SilkeAllmannLab/pacbio_snakemake

A Snakemake pipeline to go from raw .subreads.bam PacBio Iso-Seq to assembled mRNA isoforms (FASTA format)

Language: Python - Size: 5.87 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

Magdoll/CoSA

Coronavirus (SARS-Cov-2) sequencing analysis

Language: Python - Size: 2.85 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 6

nahanoo/SeqFollower

Identify inserted or deleted sequences from assemblies.

Language: Python - Size: 28.2 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

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 at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 4 - Forks: 0

Dunning-Hotopp-Lab/Dananassae_LGT

Extreme lateral gene transfer into a fly autosome

Size: 252 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

aryarm/VarBench

Benchmarking variant callers for long read data

Language: Python - Size: 105 KB - Last synced at: 4 months ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

DrQuestion/monica

MinION Open-source Nucleotide Identifier for Continuous Analysis - Software for MinION sequencing quantitative metagenomic analysis in real time

Language: Python - Size: 112 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 0

Nazeeefa/NanoSwe

NanoSwe: Analysing nanopore (PromethION) data of Swedish genomes

Language: R - Size: 93.8 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

AndreHolzer/PuntSeq Fork of d-j-k/puntseq

PuntSeq - Chasing the microbial diversity of Cambridge's freshwater

Language: HTML - Size: 482 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

mjoppich/gfold_lr

Language: C++ - Size: 147 KB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0