pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

nanopore jupyter-notebook generates-plots computing-metrics

Updated Aug 14, 2020
Python

igordot / genomics

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A collection of scripts and notes related to genomics and bioinformatics

science workflow bioinformatics nanopore genomics sequencing vcf dna fasta gtf illumina fastq fast5

Updated Jul 17, 2020
R

Psy-Fer / SquiggleKit

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SquiggleKit: A toolkit for manipulating nanopore signal data

bioinformatics nanopore

Updated Aug 28, 2020
Python

nanoporetech / bonito

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Bonito - A PyTorch Basecaller for Oxford Nanopore Reads

nanopore pytorch basecalling

Updated Sep 1, 2020
Python

giesselmann / nanopype

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Snakemake pipelines for nanopore sequencing data archiving and processing

docker workflow nanopore pipeline singularity snakemake-pipelines

Updated Aug 17, 2020
Python

hyeshik / poreplex

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A versatile sequenced read processor for nanopore direct RNA sequencing

adapter rna-seq nanopore multiplexing barcoding

Updated May 24, 2020
Python

nanoporetech / pipeline-structural-variation

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

nanopore whole-genome-sequencing structural-variation long-reads

Updated May 4, 2020
Python

nanoporetech / wub

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Tools and software library developed by the ONT Applications group

nanopore sequence-analysis nanopore-sequencing

Updated Sep 3, 2019
Python

khyox / recentrifuge

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Recentrifuge: robust comparative analysis and contamination removal for metagenomics

nanopore ngs metagenomics comparative-genomics kraken contamination clark robustness centrifuge low-biomass lmat

Updated Sep 3, 2020
Python

vpc-ccg / haslr

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

bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

Updated Apr 22, 2020
C++

nanoporetech / pipeline-transcriptome-de

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Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

rna-seq nanopore differential-gene-expression cdna differential-transcript-usage

Updated Aug 11, 2020
Python

lfaino / LoReAn

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Long Reads Annotation pipeline

rna-seq nanopore annotations pacbio

Updated Sep 1, 2020
Python

marbl / Winnowmap

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Long read / genome alignment software

nanopore pacbio genome-analysis

Updated Aug 20, 2020
C

adigenova / wengan

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An accurate and ultra-fast hybrid genome assembler

nanopore pacbio hybrid illumina genome-assembler

Updated May 25, 2020
Perl

nanoporetech / pychopper

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A tool to identify, orient, trim and rescue full length cDNA reads

rna-seq nanopore transcriptomics cdna full-length

Updated Jun 30, 2020
Python

edawson / rkmh

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Classify sequencing reads using MinHash.

bioinformatics nanopore openmp mutations minhash kmer

Updated Apr 6, 2020
C++

tleonardi / nanocompore

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RNA modifications detection from Nanopore dRNA-Seq data

bioinformatics nanopore rna-modifications

Updated Jun 5, 2020
Python

nanoporetech / pinfish

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Tools to annotate genomes using long read transcriptomics data

rna-seq nanopore genome-annotation transcriptomics cdna

Updated Apr 23, 2020
Go

enovoa / EpiNano

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Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads

nanopore rna-sequencing m6a m6a-rna-modifications direct-rna

Updated Aug 31, 2020
Python

usnistgov / mosaic

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A modular single-molecule analysis interface

python single-molecule time-series nanopore signal-processing

Updated Sep 1, 2020
Python

andrewjpage / tiptoft

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Predict plasmids from uncorrected long read data

bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

Updated Dec 5, 2019
Python

comprna / RATTLE

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Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

bioinformatics rna-seq nanopore genomics clustering transcriptome

Updated Feb 21, 2020
C++

HadrienG / nanoflow

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🔬 De novo assembly of nanopore reads using nextflow

nanopore pipeline nextflow assembly

Updated Aug 5, 2020
Nextflow

giesselmann / STRique

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Nanopore raw signal repeat detection pipeline

nanopore signal-processing

Updated Dec 16, 2019
Python

nanoporetech / pipeline-pinfish-analysis

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Pipeline for annotating genomes using long read transcriptomics data with pinfish

rna-seq nanopore genome-annotation transcriptomics cdna

Updated Apr 4, 2019
Python

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