SHARCGS statistics

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SHARCGS specifications

Information


Unique identifier OMICS_00029
Name SHARCGS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Heinz Himmelbauer <>

Publication for SHARCGS

SHARCGS in publications

 (11)
PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] a layout (l) of all the reads and their overlaps information is then constructed as a graph and (3) the consensus (c) sequence is finally inferred from the graph. software packages such as ssake, sharcgs, vcake, celera assembler, arachne, and pcap take the olc approach [,,,,,]., a de bruijn graph assembly is based on k-mer graphs from the input reads. the nodes of the graph are constituted […]

PMCID: 4573434
PMID: 26421304
DOI: 10.1155/2015/831352

[…] novo assembly). few methods to study as based on read assembly exist. however, read assembly has special roles in other biological information sciences. the typical read assembly software includes sharcgs [], ssake [], and allpaths []. the former two are assembled only for single sequence data, while the latter can be assembled for a pair of sequences from double-end sequencing. maq also […]

PMCID: 3816298
PMID: 24564274
DOI: 10.1186/1471-2105-14-S11-S5

[…] from probability theory, or from the memory-based, are gaining popularity. this was determined by zhang et. al. [] who compared the performance of eight distinct tools (i.e., ssake, vcake, qsra, sharcgs, edena, velvet, soapdenovo, and taipan) against eight groups of simulated datasets., in metagenomic studies, where there are different kinds of reads or contigs mixed together […]

PMCID: 5054208
PMID: 22768980
DOI: 10.1016/j.gpb.2012.05.006

[…] of all the reads is done to produce newer contigs. mummer aligns these newer contigs with the contigs already present in order to fill up all the remaining gaps to produce the complete genome., sharcgs stands for short-read assembler based on robust contig extension for genome sequencing . sharcgs is a de novo assembler which assumes a strong filtering of the reads to ensure […]

PMCID: 4417554
PMID: 25969752
DOI: 10.5402/2012/816402

[…] several new assemblers that are designed for short reads have recently been introduced. they can be divided into three categories: (1) greedy extension approaches, such as ssake [], vcake [], and sharcgs []; (2) overlap-layout-consensus approaches, such as edena []; (3) euler-path approaches, such as velvet [], euler-sr [], allpaths [], and abyss []. among them, euler-path approaches seem […]


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SHARCGS institution(s)
Max-Planck-Institute for Molecular Genetics, Berlin-Dahlem, Germany; Institute for Functional Genomics, Computational Diagnostics, University of Regensburg, Regensburg, Germany

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