Helixer

Gene calling with Deep Neural Networks.

Disclaimer

This software is undergoing active testing and development.

Goal

Setup and train models for ab initio prediction of gene structure. That is, to perform "gene calling" and identify which base pairs in a genome belong to the UTR/CDS/Intron of genes. Train one model for a wide variety of genomes.

Web tool

For light usage (inference on one to a few genomes), you may want to check out the Helixer web tool: https://plabipd.de/helixer_main.html and skip the installation overhead.

Install

GPU requirements

For realistically sized datasets, a GPU will be necessary for acceptable performance.

The example below and all provided models should run on an nvidia GPU with 11GB Memory (e.g. GTX 1080 Ti)

The diver for the GPU must also be installed. During development we have used

• nvidia-driver-495
• nvidia-driver-510
• nvidia-driver-525

and many in between.

via Docker / Singularity (recommended)

See https://github.com/gglyptodon/helixer-docker

Additionally, please see notes on usage, which will differ slightly from the example below.

Manual installation

Please see full installation instructions

contributors & team members

Please additionally see dev installation instructions

Example

Training and Evaluation

If the provided models don't work for your needs, information on training and evaluating the models can be found in the docs folder, as well as notes on experimental ways to fine-tune the network for target species including a hack to include RNAseq data in the input.

Inference (gene calling)

If you want to use Helixer to annotate a genome with a provided model, start here.

Using trained models

Acquire models

The best models for all lineages are best downloaded by running.

fetch_helixer_models.py

If desired, the --lineage can be specified, or --all released models can be fetched.

The available lineages are land_plant, vertebrate, invertebrate, and fungi.

Info on the downloaded models (and any new releases) can be found here: https://uni-duesseldorf.sciebo.de/s/lQTB7HYISW71Wi0

Note: to use a non-default model, set --model-filepath <path/to/model.h5>', to override the lineage default for Helixer.py.

Run on target genome

# download an example chromosome
wget ftp://ftp.ensemblgenomes.org/pub/plants/release-47/fasta/arabidopsis_lyrata/dna/Arabidopsis_lyrata.v.1.0.dna.chromosome.8.fa.gz
gunzip Arabidopsis_lyrata.v.1.0.dna.chromosome.8.fa.gz
# run all Helixer components from fa to gff3
Helixer.py --lineage land_plant --fasta-path Arabidopsis_lyrata.v.1.0.dna.chromosome.8.fa  \
  --species Arabidopsis_lyrata --gff-output-path Arabidopsis_lyrata_chromosome8_helixer.gff3

The above runs three main steps: conversion of sequence to numerical matrices in preparation (fasta2h5.py), prediction of base-wise probabilities with the Deep Learning based model (helixer/prediction/HybridModel.py), post-processing into primary gene models (helixer_post_bin). See respective help functions for additional usage information, if necessary.

Run on target genomes, 3-step method

# example broken into individual steps
fasta2h5.py --species Arabidopsis_lyrata --h5-output-path Arabidopsis_lyrata.h5 --fasta-path Arabidopsis_lyrata.v.1.0.dna.chromosome.8.fa
# the exact location ($HOME/.local/share/) of the model comes from appdirs
# the model was downloaded when fetch_helixer_models.py was called above
# this example code is for _linux_ and will need to be modified for other OSs
HybridModel.py --load-model-path $HOME/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5 \
     --test-data Arabidopsis_lyrata.h5 --overlap --val-test-batch-size 32 -v
helixer_post_bin Arabidopsis_lyrata.h5 predictions.h5 100 0.1 0.8 60 Arabidopsis_lyrata_chromosome8_helixer.gff3

Output: The main output of the above commands is the gff3 file (Arabidopsis_lyrata_chromosome8_helixer.gff3) which contains the predicted genic structure (where the exons, introns, and coding regions are for every predicted gene in the genome). You can find more about the format here. You can readily derive other files, such as a fasta file of the proteome or the transcriptome, using a standard parser, for instance gffread.

What Parameters Matter?

Most parameters from Helixer.py have been set to a reasonable default; but nevertheless there are a couple where the best setting is genome dependent.

--lineage or --model-filepath

It is of course critical to choose a model appropriate for your phylogenetic range / trained on species that generalize well to your target species. When in doubt selection via --lineage is recommended, as this will use the best available model for that lineage.

--subsequence-length and overlapping parameters

From v0.3.1 onwards these parameters are set to reasonable defaults when --lineage is used, but --subsequence-length will still need to be specified when using --model-filepath, while the overlapping parameters can be derived automatically.

Subsequence length controls how much of the genome the Neural Network can see at once, and should ideally be comfortably longer than the typical gene.

For genomes with large genes (i.e. there are frequently > 20kbp genomic loci), --subsequence-length should be increased This is particularly common for vertebrates and invertebrates but can also happen in plants. For efficiency, the overlap parameters should increase as well. It might then be necessary to decrease --batch-size if the GPU runs out of memory.

However, these should definitely not be higher than the N50, or even the N90 of the genome. Nor so high a reasonable batch size cannot be used.

General recommendations

• fungi, leave as is (--subsequence-length 21384 --overlap-offset 10692 --overlap-core-length 16038)
• plants, leave as is, or try up to --subsequence-length 106920 --overlap-offset 53460 --overlap-core-length 80190
• invertebrates, set to --subsequence-length 213840 --overlap-offset 106920 --overlap-core-length 160380
• vertebrates, set to --subsequence-length 213840 --overlap-offset 106920 --overlap-core-length 160380

--peak-threshold affects the precision <-> recall balance

In particular, increasing the peak threshold from the default of 0.8 has been reported to increase the precision of predictions, with very minimal reduction in e.g. BUSCO scores. Values such as 0.9, 0.95 and 0.975 are very reasonable to try.

Citation

Full Applicable Tool

Felix Holst, Anthony Bolger, Christopher Günther, Janina Maß, Sebastian Triesch, Felicitas Kindel, Niklas Kiel, Nima Saadat, Oliver Ebenhöh, Björn Usadel, Rainer Schwacke, Marie Bolger, Andreas P.M. Weber, Alisandra K. Denton. Helixer—de novo Prediction of Primary Eukaryotic Gene Models Combining Deep Learning and a Hidden Markov Model. bioRxiv 2023.02.06.527280; doi: https://doi.org/10.1101/2023.02.06.527280

Original Development and Description of Deep Neural Network for basewise predictions

Felix Stiehler, Marvin Steinborn, Stephan Scholz, Daniela Dey, Andreas P M Weber, Alisandra K Denton. Helixer: Cross-species gene annotation of large eukaryotic genomes using deep learning. Bioinformatics, btaa1044, https://doi.org/10.1093/bioinformatics/btaa1044