A Mapping tool using gapped minimizer and BWT FM-index

Scripts to download the PacBio, ONT and MiSeq datasets used in https://www.nature.com/articles/s41598-017-03996-z and run the pipelines as described in the paper or simply download the final assemblies as generated by the authors.

Synchronise Nanopore reads with a server.

preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.

Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

Customised reporting of ONT pinfish analysis results

Predict plasmids from uncorrected long read data

Nanopore based RNA-Seq pipeline for viral samples

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes

This repo is for the scripts used in preparation of Flongle Actinomycetes paper

Long sequencing reads classifier

De novo clustering of long transcript reads into genes

Detect and phase minor SNVs from long-read sequencing data

Documentation for running microPIPE at Pawsey

Analysis of MinION sequence data from water and sediment samples for Avian Influenza Detection

Scripts for Basecalling on GridION Sequenicng machines from Oxford Nanopore

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

The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology. PeerJ, 2022). It is meant to be the source for standalone server installation. https://doi.org/10.7717/peerj.13056

The project aims to optimize the Dynamic Time Warping (DTW) algorithm and accelerate it using Graphics Processing Units (GPUs), So that algorithm can be executed in a GPU-equipped laptop or a GPU-equipped embedded device like NVIDIA Jetson, rather than connecting to a massive server.