Long read production pipelines

An overview of all nanopack tools

Variant calling tool for long-read sequencing data

A bioinformatics tool for working with modified bases

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads

Automatic DNA methylation detection from nanopore tools and their consensus model

PacBio BAM toolkit

Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.

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

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

A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt

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

Compare transcriptomes from different species.

Automatically exported from code.google.com/p/cdhit

Toolkit for processing sequences in FASTA/Q formats

Version 5 of the CAFE phylogenetics software

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Data and scripts from the manuscript: Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees

Assembly statistic visualisation

The Composer of ggplots

Funding schemes and travel grant opportunities for postdocs

Python library to facilitate genome assembly, annotation, and comparative genomics

R interface to the JBrowse 2 Linear Genome View.

Automatic and optimised consensus clustering of one or more heterogeneous datasets

HMM-HDP models for MinION signal alignments