BiohackathonEurope2025P10

Scripts developed for Biohackathon Europe 2025 Project 10

Important links

• LRGASP online benchmarking platform

  URL: http://longbench.uv.es/

  Code: https://github.com/ConesaLab/LongTREC_LRGASP_Platform

Datasets

• PRJNA1237905

Long-read ONT-dRNA and PacBio Kinnex full-length RNA sequencing of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

• PRJNA1237905

Single-cell long-read RNA-Seq using the Kinnex (PacBio) protocol with Revio sequencing for the bone marrow of patients with AML.

• PRJNA995902

Direct Nanopore sequencing of native RNA (dRNA-seq)

Tools

Using Reference Annotation

• IsoSeq

Long-read data: Pacbio

Container: NA

Conda installation: https://anaconda.org/bioconda/isoseq

Notes: The utilization of the reference annotation is at the last step, to call different isoforms of the same gene.

• Isosceles

Long-read data: Pacbio and ONT

Container: Singularity image https://zenodo.org/records/10951160

Conda installation: NA

Notes: This is an R package.

• ESPRESSO

Long-read data: Pacbio and ONT

Container: https://hub.docker.com/r/xinglab/espresso

Conda installation: https://anaconda.org/bioconda/espresso

Notes: Snakemake pipeline also avalable.

• RATTLE

Long-read data: ONT

Container: NA

Conda installation: NA

Notes: Snakemake pipeline available. Binary compiled on Ubuntu 18.04.1 on an i7-7500U processor available at https://zenodo.org/records/6578778

• FLAIR2

Long-read data: Pacbio and ONT

Container: https://hub.docker.com/r/brookslab/flair

Conda installation: https://anaconda.org/bioconda/flair

Notes:

• Bambu

Long-read data: Pacbio and ONT

Container: NA

Conda installation: https://anaconda.org/bioconda/bioconductor-bambu

Notes: This is an R package, installed from Bioconductor. Beta for sc/spatial RNA-seq here: https://github.com/GoekeLab/bambu-singlecell-spatial

Not Using Reference Annotation

• isONclust3

Long-read data: Pacbio and ONT

Container: NA

Conda installation: https://anaconda.org/hcc/isonclust3

Notes: The installation of isONclust3 requires users to install the Rust programming language onto their system.

• Freddie

Long-read data: ONT

Container: NA

Conda installation: https://anaconda.org/bioconda/freddie

Notes: Snakemake pipeline also available. Freddie's clustering stage uses Gurobi Solver, which requires a license to use. For academics, a cost-free license is available upon registration: https://www.gurobi.com/downloads/end-user-license-agreement-academic/

Optional Use of Reference Annotation

• IsoQuant

Long-read data: Pacbio and ONT

Container: NA

Conda installation: https://anaconda.org/bioconda/isoquant

Notes:

• StringTie3

Long-read data: Pacbio

Container: https://depot.galaxyproject.org/singularity/stringtie%3A3.0.1--h00789bb_0

Conda installation: https://anaconda.org/bioconda/stringtie

Notes: