nat2bee

METEORE

Automatic DNA methylation detection from nanopore tools and their consensus model

chopper

pbtk

PacBio BAM toolkit

Hairsplitter

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

pycoQC

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

Clair3

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

ont_tutorial_basicqc

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

EpiNano

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

crossr

Compare transcriptomes from different species.

DGE_workshop

cdhit

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

seqtk

Toolkit for processing sequences in FASTA/Q formats

CAFE5

Version 5 of the CAFE phylogenetics software

Bismark

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

Foragers_vs_Nurses

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-stats

Assembly statistic visualisation

patchwork

The Composer of ggplots

postdoc-funding-schemes

Funding schemes and travel grant opportunities for postdocs

jcvi

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

JBrowseR

R interface to the JBrowse 2 Linear Genome View.

DESCHRAMBLER

clust

Automatic and optimised consensus clustering of one or more heterogeneous datasets

signalAlign

HMM-HDP models for MinION signal alignments

Lace

Building SuperTranscripts: A linear representation of transcriptome data

OrthoFinder

Phylogenetic orthology inference for comparative genomics

pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

Training-modules

Materials for short, half-day workshops

sad

Corset

Software for clustering de novo assembled transcripts and counting overlapping reads

lintr

Static Code Analysis for R