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CREST specifications


Unique identifier OMICS_00312
Alternative name Clipping REveals STructure
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Clipping REveals STructure

CREST citations


Whole exome sequencing reveals the origin and evolution of hepato cholangiocarcinoma

Nat Commun
PMCID: 5832792
PMID: 29497050
DOI: 10.1038/s41467-018-03276-y
call_split See protocol

[…] reads alignment to human reference genome and some soft-clipped reads were extracted. Then, mapping to human and virus reference genome were conducted. The HBV integration sites would be detected by clipping reveals structure (CTEST) using an assembly-mapping-searching-assembly-alignment procedure. We explored the common HBV integration sites between HCC and iCCA components within same H-ChC samp […]


The genomic landscape of pediatric myelodysplastic syndromes

Nat Commun
PMCID: 5691144
PMID: 29146900
DOI: 10.1038/s41467-017-01590-5

[…] ine mosaicism. Germline copy-number variations and structural variations were identified with the use of the Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING) and Clipping Reveals Structure (CREST) algorithms. For all SNPs and INDELs, functional prediction (e.g., SIFT, CADD, and Polyphen) and population minor allele frequency (MAF) were annotated. In this work, […]


Genomic profiling of multiple sequentially acquired tumor metastatic sites from an “exceptional responder” lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response

PMCID: 5111000
PMID: 27900369
DOI: 10.1101/mcs.a001263

[…] We used the WGS data to identify somatic chromosomal rearrangements or structural variants (SV). To reduce false positives, we used both BreakDancer () and CREST (Clipping Reveals Structure; ) to identify putative large SVs (see Supplemental Methods). We identified eight interchromosomal translocations in the lung tumor and 10 in the metastatic lymph node and o […]


Genomic heterogeneity of multiple synchronous lung cancer

Nat Commun
PMCID: 5078731
PMID: 27767028
DOI: 10.1038/ncomms13200

[…] quality >20 in both normal alleles and mutant alleles in a tumour; and (iv) median indel offsets from the end of the reads >5 bp ().For samples from patient 1, which were subjected to WGS, the CREST (Clipping Reveals Structure) algorithm was implemented to identify potential structural variants. Only breakpoint pairs with at least five supporting clipped reads spanning the breakpoints and at least […]


Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole genome next generation sequencing

BMC Genomics
PMCID: 5075209
PMID: 27769169
DOI: 10.1186/s12864-016-3153-9
call_split See protocol

[…] ) except Wt B6 which is in pure C57BL/6J background from Jackson Laboratory.The whole genome NGS raw data was first aligned to mouse mm9 reference sequences (B6 background), then, we employed CREST (‘clipping reveals structure’) to detect structural variation (SV) including deletions (DEL), inter-chromosomal translocations (CTXs) and others. CREST is an algorithm that uses NGS reads with partial a […]


The landscape of somatic mutations in Infant MLL rearranged acute lymphoblastic leukemias

Nat Genet
PMCID: 4553269
PMID: 25730765
DOI: 10.1038/ng.3230

[…] ng SNVs.Structural variations including inter-chromosomal translocations (CTX), intra-chromosomal translocations (ITX), inversions (INV), deletions (DEL), and insertions (INS) were analyzed by CREST (Clipping REveals STructure) and annotated as previously described. In addition, BreakDancer was run using the default parameters for INF013. Paired tumor/normal bam files were used to identify putativ […]


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CREST institution(s)
Department of Information Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA; Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA; Pediatric Cancer Genome Project, St Jude Children’s Research Hospital, Memphis, TN, USA; Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA

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