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/asmmahmoud/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 ./working_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 - asmmahmoud.
• Tham Cheng Yong - cytham.
• Touati Benoukraf - benoukraflab.