AneuFinder protocols

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AneuFinder specifications


Unique identifier OMICS_15772
Name AneuFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.8.0
Stability Stable
methods, stats, graphics, IRanges, GenomicRanges, Rsamtools, DNAcopy, utils, testthat, S4Vectors, GenomeInfoDb, Biostrings, BiocStyle, grDevices, GenomicAlignments, ggplot2, ggrepel, BSgenome.Hsapiens.UCSC.hg19, R(>=3.3), knitr, reshape2, foreach, BSgenome.Mmusculus.UCSC.mm10, mclust, doParallel, cowplot, ggdendro, bamsignals, AneuFinderData, ecp, ReorderCluster
Maintained Yes


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  • person_outline Floris Foijer <>

Publication for AneuFinder

AneuFinder in pipeline

PMCID: 4888403
PMID: 27246599
DOI: 10.1186/s13059-016-0976-2

[…] bam files were sorted using samtools (version 0.1.18) [] and duplicate reads were marked using bamutil (version 1.0.3). duplicate reads and ambiguous alignments (mapq >10) were filtered out using aneufinder. estimated complexity was calculated by downsampling the reads several times and determining the fraction of unique reads each time. then the number of reads sequenced (seq_reads) […]

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AneuFinder in publications

PMCID: 5773480
PMID: 29348659
DOI: 10.1038/s41467-017-02760-1

[…] fpkm values were calculated for all genes and based on these genes were assigned active (fpkm > 1) or silent (fpkm < 1) status., aligned libraries were analyzed as previously described using aneufinder r package using the following settings: low-quality alignments (mapping quality score (mapq) < 10) and duplicate reads were excluded and read counts in 2 mb variable-width bins […]

PMCID: 5400506
PMID: 28318489
DOI: 10.7554/eLife.20873.028

[…] previously () in an automated fashion (agilent bravo robot). single cell libraries were pooled an analyzed on an illumina hiseq2500 sequencer. single cell sequencing data was analyzed using aneufinder software as described previously ()., rna was isolated using the rneasy kit (qiagen). for qpcr reactions, 1 µg of total rna was used for a reverse transcriptase reaction (superscript ii, […]

PMCID: 4888403
PMID: 27246599
DOI: 10.1186/s13059-016-0976-2

[…] the reference genome is rather even which allows accurate calls of chromosome copy number.fig. 1, the copy number state of each chromosome was determined using an in-house developed algorithm called aneufinder []. briefly, this algorithm bins the mapped reads and uses a hidden markov model (hmm) to predict the copy number state (i.e. monosomic, disomic, trisomic, etc.) for each bin. […]

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AneuFinder funding source(s)
This work was supported by a Dutch Cancer Society grant (KWF grant RUG-2012-5549) and a Groningen Foundation for Paediatric Oncology (SKOG) grant, and by an NWO (The Netherlands Organisation for Scientific Research) MEERVOUD grant and a University of Groningen Rosalind Franklin Fellowship grant.

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