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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Heinz Himmelbauer <>

Publication for SHARCGS

SHARCGS citations

 (11)
library_books

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

2016
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 […]

library_books

Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico

2015
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 […]

library_books

A base composition analysis of natural patterns for the preprocessing of metagenome sequences

2013
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 […]

library_books

Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers

2012
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 […]

library_books

Enhancing De Novo Transcriptome Assembly by Incorporating Multiple Overlap Sizes

2012
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 […]

library_books

Evaluation of Methods for De Novo Genome Assembly from High Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results

2011
PMCID: 3168497
PMID: 21915294
DOI: 10.1371/journal.pone.0024182

[…] methods in this category include euler-sr , velvet and allpaths-lg . other schemes are based on a more traditional overlap and contig extension approach and include the edena method , sharcgs and vcake . these assemblers have been designed to handle small genomes, such as bacteria, and may not be directly applicable on larger more complex genomes. the abyss assembler features […]


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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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