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itap's Introduction

License: GPL v3 Don't judge me

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, 420โ€“423 (2019)

Licence

GPL v3

Authors

itap's People

Contributors

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Watchers

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