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fragScaff specifications


Unique identifier OMICS_12163
Name fragScaff
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input to fragScaff consists of an initial genome assembly (e.g., based on shotgun and mate-pair sequencing data) and data produced by CPT-seq.
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Jay Shendure

Publication for fragScaff

fragScaff citations


Chromosome scale assembly of the Monopterus genome

PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] egies for the assembly of a long scaffold have also been developed, e.g., BAC/fosmid paired end sequencing, the long-read sequencing (LRseq) [] approach, contiguity-preserving transposase sequencing (fragScaff) [], and various assembly algorithms [, ]. Recently, chromatin interactions, such as high-throughput/resolution chromosome conformation capture, have been used to assemble ultra-long scaffol […]


Draft genome of the Peruvian scallop Argopecten purpuratus

PMCID: 5905365
PMID: 29617765
DOI: 10.1093/gigascience/giy031

[…] and then all of the Illumina reads were used to correct the genome assembly by Pilon_v1.18 (Pilon, RRID:SCR_014731) for two rounds []. After that, the 10X linked-reads were used to link scaffolds by fragScaff_140 324.1 []. First, in order to solve the issue of heterozygosity, in our assembly process we chose 19-kmer to draw k-mer distribution histogram and classified all the kmers into homozygous […]


From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana)

PMCID: 5427496
PMID: 28341701
DOI: 10.1534/g3.117.040055
call_split See protocol

[…] fragScaff employs BED formatted files to ignore repeats and ambiguous bases in the definition of nodes. A RepeatMasker exclusion file was prepared using the P. lambertiana v1.0 repeat annotation descr […]


A Hybrid Approach for de novo Human Genome Sequence Assembly and Phasing

Nat Methods
PMCID: 4927370
PMID: 27159086
DOI: 10.1038/nmeth.3865

[…] en than expected by chance. By looking at the patterns of co-occurrence of reads from the same pool mapped onto the ends of scaffolds, we can identify and orient linked scaffolds. We used the program fragScaff to achieve this scaffolding, which increased the scaffold N50 of our assembly to 7.0 Mb (), representing a 12-fold improvement. […]

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fragScaff institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Illumina, Inc, Advanced Research Group, San Diego, CA, USA
fragScaff funding source(s)
Grants HG006283 and T32HG000035 from the National Human Genome Research Institute (NHGRI); graduate research fellowship DGE-0718124 from the National Science Foundation

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