BIC-seq statistics

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Citations per year

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Tool usage distribution map

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Associated diseases

Associated diseases

BIC-seq specifications


Unique identifier OMICS_03362
Name BIC-seq
Alternative name BIC-seq2
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format BAM
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


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  • person_outline Ruibin Xi <>

Publications for BIC-seq

BIC-seq in publications

PMCID: 5932867
PMID: 29720102
DOI: 10.1186/s12864-018-4709-7

[…] parameters. two methods were used to evaluate copy number variation (cnv) in each of p. ramorum isolates. the first method detects cnvs from bwa aligned reads using a read-depth algorithm called bic-seq []. to minimize experimental noise, the genome sequence isolate nd886 (cdfa1418886), an euploid isolate from camellia found in a nursery, and pr-1556, an euploid isolate from california bay, […]

PMCID: 5865353
PMID: 29566644
DOI: 10.1186/s12885-018-4199-7

[…] default parameters. fusions were called by self-developed scripts with at least 5 pairs of reads spanned over the breakpoints between two partner genes. the cnvs of tumor tissues were calculated by bic-seq2 [] with default parameters, and the cnvs of ctdna samples were called by a method reported by jacob j. chabon et al. []. all mutations were manually reviewed using igv [] […]

PMCID: 5668369
PMID: 29097733
DOI: 10.1038/s41598-017-14962-0

[…] escribed in research by bellos e et al.. we split the whole genome into bins with 500kb length and count the read depth (rd) in each bin, followed by gc normalization method described by yu z et al.. bic-seq was used for segmentation of off-target sequencing data., the experimental data are presented as the mean ± sem and were analyzed with the two-tailed student’s t test. the threshold of p <  […]

PMCID: 5590190
PMID: 28882180
DOI: 10.1186/s13046-017-0591-4

[…] or <0.1, maf threshold <1% while maf < 0.5% at hotspots), with an empirically increased requirement at repeats., a statistically rigorous and computationally efficient algorithm called bic-seq was used for detecting cnvs. in this algorithm, a poisson or other parametric models are not assumed on the read distribution as is done in other currently available methods, and it is thus […]

PMCID: 5343482
PMID: 28262751
DOI: 10.1038/ncomms14648

[…] least two of the six samples (two replicates of three conditions each) were retained to remove any non-reproducible calls., the genome was segmented based on poliii enrichment in wild-type using the bic-seq command line tool mbicseq with option ‘l 1', and providing polii and input read counts in 100 bp bins. segments with average log2-enrichment greater than 0.1 were selected as transcribed […]

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BIC-seq institution(s)
School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Center for Quantitative Biology, Peking University, Beijing, China; Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Korea
BIC-seq funding source(s)
Supported by National Institutes of Health (NIH) [R01EY024230]; Ludwig Cancer Center; National Natural Science Foundation of China [11471022 and 71532001]; National Key Basic Research Program of China [2015CB856000]; Recruitment Program of Global Youth Experts of China.

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