https://github.com/nextomics/inscan

Region based insertion detection from long reads
https://github.com/nextomics/inscan

Last synced: 14 days ago
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Region based insertion detection from long reads

• Host: GitHub
• URL: https://github.com/nextomics/inscan
• Owner: Nextomics
• License: gpl-3.0
• Created: 2018-06-11T02:02:48.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-06-21T02:16:03.000Z (over 6 years ago)
• Last Synced: 2023-10-20T22:02:57.180Z (about 1 year ago)
• Language: Python
• Homepage:
• Size: 29.3 KB
• Stars: 3
• Watchers: 7
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# inScan

inScan is devoloping for finding genomic insertion variation from long 

reads(from both Pacbio and Nanopore sequencing).

inScan differs from the published state of art Structure Variation detecting 

tools(Sniffles and NanoSV) for long reads sequencing technology in two ways. First, 

inScan can find complex insertions when the insert sequence mapped to another 

chromosome. Second, inScan detects insertions in a given region, therefore useful 

for quickly checking if there are insertions in the region(Short Tandem Repeat region

for example) of interest.

# Dependency

Python3.6.2 or later

* pysam

# Getting started

```sh

git clone [email protected]:Nextomics/inScan.git

cd inScan

python3 inScan.py input.bam input.bed output.json

```

inScan takes three positional arguments, a bam file, a bed file, a output file name.

inScan has been tested using NGMLR, BWA mem, Minimap2 output bam files. 

Generally, inScan will work for a bam file with "SA" tag.

bed file contains the regions to be tested.

output json: {"region":{"reads":[["chromosome","start","end","insert_size"],...],...},...}