Awesome Open Source

Programming Languages

Search results for python nanopore

58 search results found

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

Sequence correction provided by ONT Research

A PyTorch Basecaller for Oxford Nanopore Reads

PEPPER-Margin-DeepVariant

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

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

Identification of differential RNA modifications from nanopore direct RNA sequencing

Methylation/modified base calling separated from basecalling.

Squigglekit ⭐ 106

SquiggleKit: A toolkit for manipulating nanopore signal data

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Pipeline Transcriptome De ⭐ 95

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

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

Pipeline Structural Variation ⭐ 87

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

Recentrifuge ⭐ 83

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Research release basecalling models and configurations

Nanopype ⭐ 78

Snakemake pipelines for nanopore sequencing data archiving and processing

Pychopper ⭐ 74

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

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

Long Reads Annotation pipeline

Nanocompore ⭐ 56

RNA modifications detection from Nanopore dRNA-Seq data

Tools and software library developed by the ONT Applications group

Poreplex ⭐ 51

A versatile sequenced read processor for nanopore direct RNA sequencing

Long-reads Gap-free Chromosome-scale Assembler

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

A modular single-molecule analysis interface

Nanopore raw signal repeat detection pipeline

Graph-based assembly phasing

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

An all-in-one genome-centric metagenomics workflow using long reads

Pyguppyclient ⭐ 25

Python client library for Guppy

Pipeline Pinfish Analysis ⭐ 22

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Predict plasmids from uncorrected long read data

Clairs To ⭐ 18

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

Sturgeon ⭐ 18

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.

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

Clair3 Trio ⭐ 12

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

Modphred ⭐ 12

modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

Python bindings to spoa

Fast5seek ⭐ 11

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

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

Longread_plots ⭐ 10

A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.

Fast5_fetcher ⭐ 9

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

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

Trackcluster ⭐ 9

An analysis pipeline for Nanopore direct-RNA sequencing

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Nanosim H ⭐ 8

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

Nanometa_live ⭐ 7

A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline functionality post-initialization.

Ont Analysis Toolkit ⭐ 6

A toolkit for monitoring ONT MinION sequencing, followed by data analysis, for viral genomes amplified with tiled amplicon sequencing.

Ampligone ⭐ 6

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

Biochemical-free targeting of RNA classes during direct RNA sequencing

Nanopore direct RNA basecaller

Quality control plotting for long reads

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

Mykrobe_tb_workflow ⭐ 5

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

One-step genotyping software using a long-read sequencer

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

Clair3 Rna ⭐ 5

Clair3-RNA - long-read short variant caller for RNA sequencing data

Related Searches

Python Docker (14,113)

Python Machine Learning (14,099)

Python Deep Learning (13,092)

Python Jupyter Notebook (12,976)

Python Pytorch (7,877)

Python Classification (6,281)

Python Pandas (6,193)

Python Pipeline (4,391)

Python Bash (3,825)

Python Matplotlib (3,776)

1-58 of 58 search results

Privacy | About | Terms | Follow Us On Twitter

Copyright 2018-2024 Awesome Open Source. All rights reserved.