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Functions to process LM-PCR reads from 454/Illumina data

Bioconductor version: Release (3.19)

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

Author: Nirav V Malani <malnirav at>

Maintainer: Nirav V Malani <malnirav at>

Citation (from within R, enter citation("hiReadsProcessor")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Using hiReadsProcessor HTML R Script
Reference Manual PDF


biocViews Preprocessing, Sequencing, Software
Version 1.40.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License GPL-3
Depends R (>= 3.5.0), Biostrings, pwalign, GenomicAlignments, BiocParallel, hiAnnotator
Imports sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods
System Requirements BLAT, UCSC hg18 in 2bit format for BLAT
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Suggests knitr, testthat, markdown
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Follow Installation instructions to use this package in your R session.

Source Package hiReadsProcessor_1.40.0.tar.gz
Windows Binary
macOS Binary (x86_64) hiReadsProcessor_1.40.0.tgz
macOS Binary (arm64) hiReadsProcessor_1.40.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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