nanoinsight 0.0.3

Description:

nanoinsight 0.0.3

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.