Ub-ISAP specifications
Information
| Unique identifier | OMICS_19200 |
|---|---|
| Name | Ub-ISAP |
| Alternative name | UNIX-based vector Integration Site Analysis Pipeline |
| Software type | Pipeline/Workflow |
| Interface | Command line interface |
| Restrictions to use | None |
| 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. |
| Input format | FASTQ |
| 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. |
| Output format | Tabular format as.txt file |
| Operating system | Unix/Linux |
| Programming languages | Perl |
| Computer skills | Advanced |
| Stability | Stable |
| Requirements | cutadapt, Bowtie2, Bedtools |
| Maintained | Yes |
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Maintainer
- person_outline Atul Kamboj <>
Ub-ISAP article
library_books
Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.
2017 BMC Bioinformatics
PMID: 28623888
DOI: 10.1186/s12859-017-1719-4
Ub-ISAP 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
Ub-ISAP funding source(s)
Supported by The Kid’s Cancer Project.
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