Rich is a Python library for rich text and beautiful formatting in the terminal.

Plot structural variant signals from many BAMs and CRAMs

Short, simple, direct scripts for creating ASCII graphical histograms in the terminal.

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Download FASTQ files from SRA or ENA repositories.

2 ~ 6 sets venn diagram for python

ENCODE ChIP-seq pipeline

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

A Python command-line shell

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

oxford dot plots

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool

just annotate it, dammit!

Efficient phylogenetic clustering of viral sequences

convert various features into a GFF-like file for use in genome browsers

A 'time'-like utility for Unix that measures peak memory usage

Tools and software library developed by the ONT Applications group

Protein hint generation pipeline for gene finding in eukaryotic genomes

Frequently used commands in bioinformatics

A small python library to adjust and annotate axis ticklabels in plots.

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requ…

Simple library/pipeline to generate and handle Hi-C data.

A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.

NANOME pipeline (Nanopore long-read sequencing consensus DNA methylation detection method and pipeline)

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets