iCallSV: Structural Aberration Detection from NGS datasets

Description: Description from GitHub:

"iCallSV is a Python library and command-line software toolkit to call structural aberrations from Next Generation DNA sequencing data. Behind the scenes it uses Delly2 to do structural variant calling. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina."

Subject(s)

Access via GitHub
MSKCC GitHub fork

Access via GitHub
Author's GitHub

Access via iCallSV Wiki
GitHub documentation

Access via Zenodo
Access Restrictions: Free to All
Access Instructions: Available to download and use under an Apache 2.0 License
DOI: 10.5281/zenodo.184864
Associated Publications: Hu K, Yu W, Ajayi OE, Li L, Huang Z, Rong Q, Wang S, Wu QF. Integrated analysis of whole genome and transcriptome sequencing in a young patient with gastric cancer provides insights for precision therapy. Oncol Lett. 2020 Oct;20(4):115. Epub 2020 Aug 12. PMID: 32863928; PMCID: PMC7448559.
Software Used: BioPython
Tools for biological computation written in Python

coloredlogs
Enables colored terminal output for Python’s logging module

Delly
Structural variant discovery by integrated paired-end and split-read analysis

iAnnotateSV
Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data

pandas
open source data analysis and manipulation tool, built on top of the Python programming language.

pysam
Python package for reading, manipulating, and writing genomic data sets

PyVCF
Variant Call Format (VCF) parser for Python

targetSeqView
Evaluate structural rearrangement calls from a candidate lists
Dataset Format(s): R, TXT, PY
Dataset Size: 565 KB