Repeat annotation tool for insertions called by NanoVar
Project description
NanoINSight
NanoINSight is a repeat annotation tool for insertions called by NanoVar.
Installation:
Option 1: Using Pip
pip install nanoinsight
Option 2: Cloning from GitHub repository
git clone https://github.com/benoukraflab/nanoinsight.git
cd nanoinsight
pip install .
Installation of dependencies
1. MAFFT
Option 1: Conda
conda install -c bioconda mafft
Option 2:
Please visit here to download the "without_extensions" source package and visit here for instructions to install.
- Please note that MAFFT source package with extnesions is not needed as it supports RNA structural alignments.
- Path of executable binary is needed. You can get it by typing "which mafft" in the terminal window.
2. RepeatMasker
Option 1: Conda
conda install -c bioconda repeatmasker
Option 2:
Please visit here for instructions to install.
Run:
Option 1: Run with NanoVar command by adding the "--annotate_ins [species]" parameter
nanovar [Options] --annotate_ins human sample.fq/sample.bam ref.fa working_dir
For more details: see NanoVar wiki
Option 2: Run via the command-line
nanoinsight [-h] [-v] [-q] [-t int] [-i path] [-u path] [-m path] [-r path]
[-s species] [VCF] [working_directory]
Example:
nanoinsight -t 4 -s human sample.nanovar.pass.vcf ./work_dir
Required parameters:
Parameter | Description |
---|---|
-s | Specify species for repeatmasker (e.g. human) |
[VCF] | Path to VCF input file |
[working_directory] | Path to working directory |
Additional Parameters:
Parameter | Description |
---|---|
-h | Show help message |
-v | Show version |
-q | hide verbose |
-t | Number of threads to be used [1] |
-i | Path to ins_seq.fa file (NanoVar output) |
-u | Path to sv_support_reads.tsv file (NanoVar output) |
-m | Path to mafft executable file |
-r | Path to RepeatMasker executable file |
Output:
Output | Description |
---|---|
.ins.con.fasta | fasta file of consensus sequences of insertions found in the VCF input file |
rm_output | output directory of RepeatMasker |
Citation:
If you use NanoINSight, please cite:
Authors:
- Asmaa Samy - AsmaaSamyMohamedMahmoud.
- Tham Cheng Yong - cytham.
- Touati Benoukraf - benoukraflab.
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