NanoINSight

NanoINSight is a repeat annotation tool for insertions called by NanoVar.

Installation:

Option 1:

Installing NanoVar v1.6 from PyPI will automatically install NanoINSight, Please visit here for instructions to install NanoVar.

Option 2: Using Pip

pip install nanoinsight

Option 3: 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

Authors:

Asmaa Samy - AsmaaSamyMohamedMahmoud.
Tham Cheng Yong - cytham.
Touati Benoukraf - benoukraflab.

benoukraflab / nanoinsight Goto Github PK

nanoinsight's Introduction

NanoINSight

Installation:

Option 1:

Option 2: Using Pip

Option 3: Cloning from GitHub repository

Installation of dependencies

1. MAFFT

Option 1: Conda

Option 2:

2. RepeatMasker

Option 1: Conda

Option 2:

Run:

Option 1: Run with NanoVar command by adding the "--annotate_ins [species]" parameter

Option 2: Run via the command-line

Output:

Authors:

nanoinsight's People

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