Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: nanopore

Repositories

3w1714n0/Benchmark_Analysis_full-length_isoforms

Benchmark analysis of algorithms for determining full-length mRNA isoforms by Nanopore RNA-seq data.

Language: R - Size: 262 KB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

Han-Cao/HarmoniSV

A toolkit to harmonize and filter structural variations across methods and samples.

Language: Python - Size: 5.51 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

Psy-Fer/interARTIC

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Language: CSS - Size: 85.3 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 24 - Forks: 3

nanoporetech/pipeline-pinfish-analysis 📦

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Language: Python - Size: 137 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 27 - Forks: 5

lfaino/LoReAn

Long Reads Annotation pipeline

Language: Python - Size: 467 MB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 68 - Forks: 10

HKU-BAL/ClusterV

ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data

Language: Python - Size: 13.5 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 5 - Forks: 0

yanhui09/laca

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

Language: Python - Size: 124 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 2

garcia-nacho/Wastewater_SARS-CoV-2

Surveillance of wastewater for SARS-CoV-2 detection

Language: R - Size: 18.2 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 1

nanoporetech/pyguppyclient 📦

Python client library for Guppy

Language: Python - Size: 93.8 KB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 30 - Forks: 5

decacent/PyNanoLab

all in one GUI software for data analysis and visualization

Size: 225 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 10 - Forks: 1

mbhall88/tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Language: Python - Size: 3.3 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 11 - Forks: 2

GoekeLab/bambu

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

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

microgenlab/porefile

A Nextflow full-length 16S profiling pipeline for ONT reads

Language: Nextflow - Size: 7.57 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 19 - Forks: 4

The R package "sarlacc" contains a pipeline to analyse nanopore sequencing data. It trims adapter sequences, retrieves optional UMI's, clusters reads and produces a consensus sequence for each cluster after multiple sequence alignment.

Language: R - Size: 534 KB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 13 - Forks: 5

nanoporetech/pinfish 📦

Tools to annotate genomes using long read transcriptomics data

Language: Go - Size: 120 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 43 - Forks: 13

shelkmike/Elloreas

Elloreas, a genome assembler

Language: Perl - Size: 915 KB - Last synced at: 8 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

kangaroo96/osbp_detect

osbp_detect: Extract OsBp translocation events from ONT bulk FAST5

Language: Python - Size: 47.9 KB - Last synced at: 8 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

iqbal-lab-org/Mykrobe_tb_workflow

A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe

Language: Python - Size: 6.98 MB - Last synced at: 8 months ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 3

edawson/rkmh

Classify sequencing reads using MinHash.

Language: C++ - Size: 33.3 MB - Last synced at: 8 months ago - Pushed at: about 4 years ago - Stars: 43 - Forks: 4

giesselmann/STRique 📦

Nanopore raw signal repeat detection pipeline

Language: Python - Size: 1.48 MB - Last synced at: 7 months ago - Pushed at: about 1 year ago - Stars: 41 - Forks: 10

Scaramir/Covid-Assembly

Project 2 from SC2 @ FUB This project is currently still in progress, therefore the code is not cleaned yet and still contains some unnecessary comments.

Language: Python - Size: 175 KB - Last synced at: 5 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

punamrattu/computational_biophysics

Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).

Language: Shell - Size: 20.5 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

vpc-ccg/haslr

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

Language: C++ - Size: 155 KB - Last synced at: 8 months ago - Pushed at: about 4 years ago - Stars: 73 - Forks: 9

SLI239/nanopore_transcript_quantification

Transcript Reconstruction and Quantification from Oxford Nanopore RNA Sequencing Dataset

Language: Nextflow - Size: 57.6 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

biocorecrg/ropes-linux-mop2-2023

Course for ROPES summer school, May 2023

Language: Nextflow - Size: 98.9 MB - Last synced at: 10 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

TF-Chan-Lab/LAFITE

tool for long read transcriptome assembly

Language: Jupyter Notebook - Size: 46.5 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 3 - Forks: 1

BatistaLab/Exon9A_Nanopore

Nanopore direct RNA sequencing for cryptic splice mutation in HLRCC

Language: HTML - Size: 730 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

ganlab/GALA

Long-reads Gap-free Chromosome-scale Assembler

Language: Python - Size: 4.87 MB - Last synced at: 8 months ago - Pushed at: about 1 year ago - Stars: 60 - Forks: 12

mbhall88/tubby-manuscript

Manuscript for our work training and evaluating a Mycobacterium tuberculosis-specific Nanopore basecalling model

Language: HTML - Size: 876 KB - Last synced at: 10 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

mbhall88/head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.

Language: Jupyter Notebook - Size: 501 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 2

marcDabad/snakemake_nanometh

snakemake pipeline based on nanopolish

Language: Python - Size: 50.8 KB - Last synced at: 10 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

HadrienG/nanoflow 📦

:microscope: De novo assembly of nanopore reads using nextflow

Language: Nextflow - Size: 4.23 MB - Last synced at: 10 months ago - Pushed at: almost 4 years ago - Stars: 20 - Forks: 3

salrodgom/lammps_RASPA_interface

Language: Fortran - Size: 10.4 MB - Last synced at: 10 months ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 1

etheleon/deepore

Nanopore base caller based on original Chiron adding Dropout and SRU

Language: Python - Size: 27.8 MB - Last synced at: 10 months ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

Shians/PorexploreR

Bob Loblaw's Law Blog Applauds Porexplorer

Language: R - Size: 4.68 MB - Last synced at: 10 months ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

jeremyButtler/find--Co-infections

A pipeline to detect co-infections from Nanopore reads.

Language: C - Size: 5.06 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0

ssnl-anu/poremaker

Matlab code for the GUI for simple and cost-effective nanopore fabrication platform.

Size: 168 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

jeremyButtler/fqGetIds

A program using SMID vectors to extract fastq reads by read ids.

Language: C - Size: 484 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

EverymanBio/pestalotiopsis

Assembly and phylogentic analysis pipeline for draft genome of a Pestalotiopsis fungi.

Language: Python - Size: 205 KB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 2

iqbal-lab-org/tb-sputum-project

Pipeline to analyse the TB sputum data

Language: Jupyter Notebook - Size: 13.7 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

giesselmann/nanopype 📦

Snakemake pipelines for nanopore sequencing data archiving and processing

Language: Python - Size: 23.2 MB - Last synced at: 8 months ago - Pushed at: over 2 years ago - Stars: 87 - Forks: 15

shadowk29/CUSUM

Implements a modified version of the CUSUM algorithm for robust detection of step-like changes time-series data

Language: C - Size: 2.12 MB - Last synced at: 8 months ago - Pushed at: almost 4 years ago - Stars: 8 - Forks: 6

thanhleviet/nf-ont-taxamap

Taxonomic profiling ONT metagenomics reads using minimap2

Language: Nextflow - Size: 57.6 KB - Last synced at: 5 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1

adigenova/wengan

An accurate and ultra-fast hybrid genome assembler

Language: Perl - Size: 141 KB - Last synced at: 8 months ago - Pushed at: over 3 years ago - Stars: 82 - Forks: 13

vibaotram/baseDmux

snakemake workflow for basecalling and demultiplexing of ONT sequencing data

Language: Python - Size: 84.2 MB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1

nanoporetech/pyspoa

Python bindings to spoa

Language: Python - Size: 45.9 KB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 12 - Forks: 3

nanoporetech/epi2me-api

API for communicating with the EPI2ME Platform for nanopore data analysis. Used by EPI2ME Agent & CLI.

Language: TypeScript - Size: 61.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 7

eleni-chr/long-read-RNA-seq-plotting-suite

Various functions to inspect, extract, and visualise long-read RNA-seq data.

Language: MATLAB - Size: 72.3 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

ioannisa92/Nanopore_modification_inference

Graph Convolution based model for de novo identification of nucleotide modifications

Language: Python - Size: 156 MB - Last synced at: 8 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 0

gaarangoa/nanoARG

antibiotic resistance profiling of nanopore reads

Language: HTML - Size: 82.4 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

colindaven/guppy_on_slurm

Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler

Language: Shell - Size: 47.9 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 13 - Forks: 5

jnoms/SV40_transcriptome

Toolkit and pipeline for processing short- and long-read RNA sequencing data.

Language: Jupyter Notebook - Size: 4.36 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

GoekeLab/NanoporeRNASeq

Nanopore RNASeq data

Language: R - Size: 107 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

CarolinaPB/nanopore-assembly

Pipeline to assemble oxford nanopore long sequencing reads and perform variant calling with long and short reads

Language: Python - Size: 1.55 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 0

weir12/DENA

Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.

Language: Python - Size: 323 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 17 - Forks: 4

mbhall88/fast5seek 📦

Subset of fast5 files contained in a fastq, BAM, or SAM file.

Language: Python - Size: 4.05 MB - Last synced at: 11 days ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 2

KevinMenden/hybrid-assembly

Pipeline for hybrid assembly using short and long reads.

Language: Nextflow - Size: 83 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 5

smaegol/nanotail

R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions

Language: R - Size: 20.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 7 - Forks: 5

HKU-BAL/ONT-TB-NF

Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.

Language: Nextflow - Size: 1.89 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 2 - 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 at: 2 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

darelab2014/Dinopore

DInoPORE: Direct detection of INOsines in native RNA with nanoPORE sequencing

Language: R - Size: 39.6 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 2

cihanerkut/shanti

Shallow Nanopore Sequencing for Transcriptomics

Language: Nextflow - Size: 22.5 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

nodrogluap/MinNO

Automatically stop a MinION sequencing experiment after a specific amount of data has been collected.

Language: C - Size: 52.7 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

comprna/CHEUI-public

Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing

Size: 33.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

leahkemp/ont_human_workflow

A generic best practice workflow for processing human Oxford Nanopore Technologies (ONT) sequencing data.

Language: Shell - Size: 125 KB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

LRB-IIMCB/yeast_deadenylation_methods_chapter

Transcriptome-wide analysis of mRNA adenylation status in yeast using nanopore sequencing - materials accompanying the methods chapter

Language: TeX - Size: 15.6 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mbhall88/Longitude_pipeline 📦

Pipeline for analysing M. tuberculosis nanopore reads and getting drug susceptibility information.

Language: Python - Size: 2.45 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 0

CGL-Deeplearning/alleleSelector 📦

Language: Python - Size: 255 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

nanoporetech/pipeline-pychopper 📦

Utility pipeline for running pychopper, a tool to identify full length cDNA reads

Language: Python - Size: 70.3 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

Blosberg/nanopiper

(long read) fastq input to final report

Language: R - Size: 3.06 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

marabouboy/FLAME

FLAME: Full Length Adjecency Matrix Enumeration - is a module that allows for the analysis of ONT Nanopore RNA long-read sequencing data.

Language: Python - Size: 11.9 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 1

angelovangel/nanotimes

work with the time stamps of Oxford Nanopore (ONT) fastq files

Language: Rust - Size: 13.7 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

TimD1/nPoRe

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

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

comprna/radian

Nanopore direct RNA basecaller

Language: Python - Size: 70.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 2

leahkemp/guinea_pore_c

Analysis documentation for part of the reference genome assembly of the humble guinea pig. Oxford Nanopore Technologies (ONT) pore-c data.

Language: HTML - Size: 12 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

nanoporetech/homebrew-tap

Homebrew casks for applications from Oxford Nanopore Technologies PLC and Metrichor Ltd.

Language: Ruby - Size: 216 KB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 4 - Forks: 0

akikuno/DAJIN

One-step genotyping software using a long-read sequencer

Language: Python - Size: 36.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 2

Psy-Fer/fast5_fetcher

A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency

Language: Python - Size: 1.03 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 14 - Forks: 4

mbhall88/container_recipes

Repository with all my container recipes 👩‍🍳

Language: Dockerfile - Size: 98.6 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 14 - Forks: 6

bioinformagic/monica

MinION Open Nucleotide Identifier for Continuous Analysis - an open source pathogen identifier for real-time analysis on MinION output

Language: Python - Size: 1.29 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 8 - Forks: 0

mjoppich/sequ-into Fork of %{name} igemsoftware2018/igem_munich_2018

Third generation sequencing techniques rapidly evolved as a common practice in molecular biology. Great advances have been made in terms of feasibility, cost, throughput, and read-length. However, sample contamination still poses a big issue: it complicates correct, high-quality downstream analysis of sequencing data and usage in medical applications. Furthermore, it might be unclear weather the sequenced reads represent the intended target. To address these issues we developed a cross-platform desktop application: Sequ-Into.

Language: TypeScript - Size: 42 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 1