Beast code in Giters

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

Language:PythonGPL-3.0249 5 98

pepper

PEPPER-Margin-DeepVariant

Language:PythonMIT234 10 195

Clair3

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

Language:Python230 10 280

NanoSim

Nanopore sequence read simulator

Language:PythonNOASSERTION223 16 162

BBMap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

Language:JavaNOASSERTION205 11 37

rasusa

Randomly subsample sequencing reads or alignments

Language:RustMIT197 7 39

Long-read-assembler-comparison

Benchmarking of long-read assembly tools for bacterial whole genomes

Language:PythonCC-BY-4.0169 15 4

spoa

SIMD partial order alignment tool/library

Language:C++MIT153 16 51

TRF

Tandem Repeats Finder: a program to analyze DNA sequences

Language:CAGPL-3.0142 7 23

alfred

BAM Statistics, Feature Counting and Annotation

Language:C++BSD-3-Clause135 9 44

Perfect-bacterial-genome-tutorial

Language:Python118 4 11

DeepSimulator

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

Language:C112 8 51

mockcommunity

Long-read mock community experiments

Language:HTML102 9 9

MelBioInf_docs

Melbourne Bioinformatics documentation in markdown format

Language:HTML95 19 17

BAM-tricks

Tip and tricks for BAM files

80 90

data-science-sequencing.github.io

Web site for the class EE 372 : Data Science for High-Throughput Sequencing at Stanford

Language:Jupyter Notebook65 10 1

August-2019-consensus-accuracy-update

A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

Language:PythonGPL-3.056 7 2

assembly_accuracy

tools for assessing the accuracy of genome assemblies

Language:PythonMIT34 4 3

score-assemblies

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)

Language:PythonMIT24 3 9

ont-assembly-snake

Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools

Language:PythonMIT18 4 16

CONNET

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

Language:Python12 4 8

nanopore_assembly_and_polishing_assessment

Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of assembly and polishing

Language:PythonMIT12 20

signalAlign

HMM-HDP models for MinION signal alignments

Language:CMIT600