itap: fast and accurate annotation of venom gland transcriptome

Introduction

Venom gland transcriptome annotation is the process of identifying putatives toxin-like peptides in a set a transcriptomic sequences, and labelling them with family, presence/absence signal information. itap (Improved Transcriptome Annotation Pipeline) is a software tool to annotate spider venom gland transcriptome and will suport in next release cone, scorpions and other well-known venomous animal venom gland transcriptome. itap produces standards-compliant output files.

Installation

Linux or MAC based OS

# Install perl packages
sudo cpanm Bio::Perl Text::CSV::Hashify Readonly File::Copy Getopt::Declare File::Spec

# Install kallisto
See https://pachterlab.github.io/kallisto/download

# Install hmmsearch
See https://hmmer.org

# Install hmmcompete
See https://www.mdpi.com/2072-6651/9/8/245/s1
or https://github.com/koualab/hmmcompete

# Download itap
git clone https://github.com/koualab/itap.git $HOME/itap

# Copy itap to bin folder and hmm db to db folder
sudo cp itap /usr/local/bin
sudo mkdir /usr/share/itap/db
sudo cp itap/db/* /usr/share/itap/db

# Add path to $PATH
echo "$PATH:/usr/share/itap/db/" >> ~/.bashrc

Test

• Type itap -help and it should output its help screen.
• Type itap -version and you should see an output like itap version 0.1 (Tue Dec 29 14:17:51 2020).

Invoking itap

itap -t transcripts.fa.gz -f reads_R1.fq.gz -r reads_R2.fq.gz

Output files

Command line options

General:
	--transcripts, -t    Specify transcriptome file [required]
	--forward_reads, -f  Specify forward reads file [required]
	--reverse_reads, -r  Specify reverse reads file [required]

Outputs:
	--outdir, -o  Specify output folder name
	--dbdir       Specify path to databases folder
	--force       Force reuse of output folder

Setup:
	--hmm         Specify the path to personal hmm lib
	--quiet       Decrease verbosity

Computation:
	--cpus        Specify number of threads

Standard meta-options:
	--version, -v   Print program version and exit
	--usage, -u     Print program usage and exit
	--man           Print man page
	--help, -h      Print help and exit

Bugs

Submit problems or requests to the Issue Tracker.

Dependencies

Mandatory

• BioPerl
  Used for I/O fasta files.
  Stajich et al, The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct;12(10):1611-8.

• hmmcompete
  Used for precursors sequences identification and classification.
  Koua, D.; Kuhn-Nentwig, L. Spider Neurotoxins, Short Linear Cationic Peptides and Venom Protein Classification Improved by an Automated Competition between Exhaustive Profile HMM Classifiers. Toxins 2017, 9, 245.

• SignalP
  Used to find signal peptide in precursors sequences.
  Almagro Armenteros et al, SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol 37, 420–423 (2019)

Licence

GPL v3

Authors

• Anicet Ebou
• Dominique Koua