Fulcrum specifications

Information


Unique identifier OMICS_01049
Name Fulcrum
Alternative name Fulcrum Read Collapser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 043
Stability Stable
Source code URL http://pringlelab.stanford.edu/project%20files/fulcrum_v_043.tar.gz
Maintained Yes

Versioning


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Maintainer


  • person_outline Erik Lehnert <>

Publication for Fulcrum

Fulcrum in publications

 (3)
PMCID: 5357343
PMID: 28321364
DOI: 10.7717/peerj.3091

[…] identified, after which one read from each cluster is retained and others are discarded. a number of widely used programs are based on this approach, including bigpre (), cd-hit-454 (), fastuniq (), fulcrum (), jatac (). these programs were developed and are used mainly for the 454 sequencing technology, where the number of reads is moderate (from thousands to millions) and it is feasible […]

PMCID: 5123249
PMID: 28185553
DOI: 10.1186/s12859-016-1192-5

[…] must be compared to all other sequences in the dataset. this is the reason why heuristics are defined and adopted to deal with the computational challenge., fastx-toolkit collapser [], fastuniq [], fulcrum [] and cd-hit [–] are all examples of tools that implement an alignment-free strategy. fastx-toolkit collapser is able to identify and remove identical sequences from single-end reads. […]

PMCID: 4447899
PMID: 26021914
DOI: 10.1128/genomeA.00220-15

[…] (6.2 million 3-kb-, 6.2 million 5-kb-, 5.3 million 10-kb-, and 6.0 million 15-kb-long-insert read pairs), respectively, using illumina hiseq and miseq sequencers. the read pairs were dereplicated by fulcrum () and assembled using the spades assembler (). the assembly of the dereplicated read pairs by using 21 to 89 bp for the k-mer size option yielded a set of 104 contigs of ≥1 kb, whose total […]


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Fulcrum institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Fulcrum funding source(s)
Supported by Gordon and Betty Moore Foundation (#2629), National Institutes of Health (5 T32 HG000044); National Science Foundation (Graduate Research Fellowship).

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