Ub-ISAP specifications
- Unique identifier:
- OMICS_19200
- Software type:
- Pipeline/Workflow
- Restrictions to use:
- None
- Input format:
- FASTQ
- Output format:
- Tabular format as.txt file
- Programming languages:
- Perl
- Stability:
- Stable
- Maintained:
- Yes
- Name:
- UNIX-based vector Integration Site Analysis Pipeline
- Interface:
- Command line interface
- Input data:
- Multiple raw next-generation sequencing (NGS) reads in a single (single reads or paired-end reads), the 5′ TR primer and the 3′ distal primer sequences used in library preparation.
- Output data:
- Chromosomal positioning, closest gene accession number, symbol from the processed reads in, and the unique ISs characterized as transcription start site (TSS) proximal, intragenic or intergenic.
- Operating system:
- Unix/Linux
- Computer skills:
- Advanced
- Requirements:
- cutadapt, Bowtie2, Bedtools
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Ub-ISAP distribution
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Ub-ISAP support
Maintainer
- Atul Kamboj <>
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Publications
-
(Kamboj et al., 2017)
Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.
BMC Bioinformatics.
PMID: 28623888 DOI: 10.1186/s12859-017-1719-4
Institution(s)
Children’s Cancer Research Unit, Kid’s Research Institute, The Children’s Hospital at Westmead, Westmead, NSW, Australia; Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Westmead, NSW, Australia; The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, NSW, Australia; Cancer Centre for Children, The Children’s Hospital, Westmead, NSW, Australia
Funding source(s)
Supported by The Kid’s Cancer Project.
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