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hiReadsProcessor specifications


Unique identifier OMICS_16071
Name hiReadsProcessor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data Parameters for demultiplexing and sample metadata.
Output format XLS, TXT
Operating system Unix/Linux, Mac OS
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.16.0
Stability Stable
methods, BiocGenerics, GenomicRanges, testthat, Biostrings, GenomicAlignments, dplyr, BiocParallel, knitr, R(>=3.0), hiAnnotator, sonicLength, rSFFreader, readxl
Maintained Yes




No version available



  • person_outline Nirav Malani <>

hiReadsProcessor citation


HIV latency and integration site placement in five cell based models

PMCID: 3765678
PMID: 23953889
DOI: 10.1186/1742-4690-10-90

[…] with restriction enzymes msei and tsp509 and ligated to adapters. proviral ltr-host genome junctions were sequenced by 454 pyrosequencing after nested pcr., all datasets were processed using the hireadsprocessor r package []. adaptor trimmed reads were aligned to ucsc freeze hg19 using blat []. genomic alignments were scored and required to start within the first three bases of a read […]

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