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genomics

igordot /genomics

A collection of scripts and notes related to genomics and bioinformatics

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

UpdatedFeb 10, 2025
R

novoalab /modPhred

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

nanopore dna rna fast5 on-the-fly modifications basecalling guppy

UpdatedApr 29, 2024
Python

Psy-Fer /fast5_fetcher

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

UpdatedFeb 13, 2019
Python

mbhall88 /fast5seek

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

bioinformatics nanopore sam bam fastq fast5 ont

UpdatedMar 29, 2023
Python

rnajena /read5

Wrapper to read fast5, slow5, blow5 and pod5 files.

raw-data oxford-nanopore fast5 ont oxford-nanopore-data pod5 blow5 slow5

UpdatedNov 27, 2024
Python

bsaintjo /slow5-rs

Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output

rust bioinformatics nanopore genomics ffi computational-biology compbio oxford-nanopore oxford fast5 nanopore-sequencing

UpdatedNov 5, 2024
Rust

CMU-SAFARI /Molecules2Variations

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al.https…

bioinformatics quality-control sequencing sam smith-waterman needleman-wunsch vcf fasta variant-calling wfa illumina fastq genome-analysis fast5 sequence-alignment read-mapping hifi minimap2 basecalling wavefront-alignment

UpdatedJun 14, 2022

bsaintjo /pod5-rs

Rust library to support interacting with Oxford Nanopore POD5 files

genomics fast5 nanopore-sequencing long-read-sequencing pod5

UpdatedFeb 21, 2025
Rust

mbhall88 /tinysink

Synchronise Nanopore reads with a server.

oxford-nanopore fast5 bioinformatics-scripts

UpdatedApr 18, 2018
Shell

rnajena /read5_ont

Wrapper to read fast5 and pod5 files.

raw-data oxford-nanopore fast5 ont oxford-nanopore-data pod5

UpdatedNov 27, 2024
Python

Shians /PorexploreR

Bob Loblaw's Law Blog Applauds Porexplorer

bioinformatics r nanopore fast5

UpdatedJun 20, 2019
R

asadprodhan /Dorado-basecalled-reads-improve-old-bacterial-genome-assembly

Dorado-basecalled reads improve old bacterial genome assembly

nanopore fastq fast5 nanopore-sequencing basecalling nanopore-analysis-pipeline pod5

UpdatedJun 1, 2024

JannesSP /read5.github.io

Documentation for thehttps://github.com/JannesSP/read5 repository

documentation oxford-nanopore fast5 pod5 blow5 slow5 read5

UpdatedMar 5, 2024
HTML

novoalab /nanoRMS2

nanoRMS2 is a pipeline for detection of DNA/RNA modifications from raw ONT data

machine-learning nanopore dna semi-supervised-learning rna features stoichiometry fast5 modifications basecalling

UpdatedFeb 5, 2025
Python

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