Scallop specifications


Unique identifier OMICS_30128
Name Scallop
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.10.2
Stability Stable
Maintained Yes




No version available



  • person_outline Carl Kingsford
  • person_outline Dan DeBlasio

Additional information

A parameter advisor for Scallop is available on Github at

Publications for Scallop

Scallop citations


Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly

PMCID: 5848817
PMID: 29342277
DOI: 10.1093/gigascience/gix137

[…] -end reads from both libraries in addition to 2 publicly available A. ocellaris transcriptome sequencing data (SRR5253145 and SRR5253146, Bioproject ID: PRJNA374650) were individually assembled using Scallop v0.10.2 [] based on HiSat2 [] alignment of RNA-sequencing reads to the newly generated A. ocellaris genome. The transcriptome assemblies were subsequently merged using the tr2aacds pipeline fr […]


Large scale SNP discovery and construction of a high density genetic map of Colossoma macropomum through genotyping by sequencing

Sci Rep
PMCID: 5384230
PMID: 28387238
DOI: 10.1038/srep46112

[…] ruction using the GBS approach have been conducted in a number of aquaculture species including Asian seabass (Lates calcarifer), common pandora (Pagellus erythrinus), sablefish (Anoplopoma fimbria), scallop (Chlamys farreri), oysters (Crassostrea gigas × Crassostrea angulata), and small abalone (Haliotis diversicolor). This tambaqui genetic map will be valuable for genomic research and genetic en […]

Scallop institution(s)
Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
Scallop funding source(s)
Supported in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554, by the US National Science Foundation (CCF-1256087 and CCF-1319998) and by the US National Institutes of Health (R01HG007104 and R01GM122935) and by The Shurl and Kay Curci Foundation.

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