A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

A go package for generating online histograms and plotting them in the terminal and PDFs

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

A package for simulating RNA-seq library preparation with parameter estimation

An R package for the Monte Carlo simulation of sequence evolution

pcrcoal is an R package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997)

The Ensembl Compara Perl API and SQL schema

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

A tool for de novo clustering of long transcriptomic reads

biogo is a bioinformatics library for Go

Pipeline for de novo clustering of long transcriptomic reads

A tool to identify, orient, trim and rescue full length cDNA reads

Tools and software library developed by the ONT Applications group

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Tools to annotate genomes using long read transcriptomics data

A package for training strand-specific profile HMMs for primer sets from real Nanopore data

Pipeline for calling poly(A) tail lengths from nanopore direct RNA data using nanopolish

Pipeline for testing shifts in poly(A) tail lengths estimated by nanopolish

PAT-seq manuscript

Analysis pipeline for assesing biasing factors in Illumina RNA-seq protocols through realistic simulations

An R package simulating the evolution of copy number profiles along a tree

Pipeline for simulating NG-SAM experiments