MIP Scaffolder statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MIP Scaffolder
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Tool usage distribution map

This map represents all the scientific publications referring to MIP Scaffolder per scientific context
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MIP Scaffolder specifications

Information


Unique identifier OMICS_00044
Name MIP Scaffolder
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

Publication for MIP Scaffolder

MIP Scaffolder citations

 (6)
library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] fold graph have a minimum and maximum estimated length, derived from the library information. The MIP source code, along with usage instructions, is available at https://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/.Opera (): takes as inputs a collection of contigs and mapped reads and generates a scaffold graph based on the paired-end information. Frist, the program filters the connections betwee […]

library_books

Unravelling the genome of Holy basil: an “incomparable” “elixir of life” of traditional Indian medicine

2015
BMC Genomics
PMCID: 4445982
PMID: 26017011
DOI: 10.1186/s12864-015-1640-z

[…] A v1.4.6 [] tool. Super-scaffolding was performed in order to merge the existing gap-closed scaffolds into super-scaffolds using relative orientation of SOLiD mate pair reads. Super-scaffolding using MIP-scaffolder [] requires F3 and R3 reads to be mapped on preassembled scaffolds. This was achieved using SHRiMP2 [] tool, which aligns reads in colorspace format. […]

library_books

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

2014
Nat Commun
PMCID: 4164777
PMID: 25189940
DOI: 10.1038/ncomms5737

[…] s.Error-corrected 454 and Illumina PE reads were assembled using Newbler (Roche) and SOAPdenovo (). Contigs with a minimal length of 500 bp were used in scaffolding. For scaffolding, we used in-house MIP Scaffolder software, and required at least two read pairs for connecting a pair of contigs. Scaffolding was performed in seven stages in which the PE and MP libraries were added in ascending order […]

library_books

Next Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

2013
PLoS Comput Biol
PMCID: 3861042
PMID: 24348224
DOI: 10.1371/journal.pcbi.1003345

[…] ts . Some assemblers include scaffolding modules (e.g., Euler-SR, ALLPATHS-LG, Velvet, SGA, SOAPdenovo, and Shorty) (see ) while others are stand-alone scaffolders such as Bambus , , SSPACE , SOPRA , MIP scaffolder , Opera , and SCARPA (see ).There are many challenges currently facing the stand-alone scaffolders such as using of different paired-end libraries with different insert sizes, dealing […]

library_books

ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

2013
BMC Genomics
PMCID: 3651407
PMID: 23627759
DOI: 10.1186/1471-2164-14-289

[…] in some extreme cases, no gap truly existed between two such “contigs”. Several existing scaffolders for high throughput sequencing (HTS) genome assemblies, such as GRASS [], SSPACE [], OPERA [] and MIP Scaffolder [], may provide effective scaffolding; however, they lack global visualization and have to face the balance between scaffold length and accuracy. Most visualization tools, such as Conse […]

library_books

Normalized N50 assembly metric using gap restricted co linear chaining

2012
BMC Bioinformatics
PMCID: 3556137
PMID: 23031320
DOI: 10.1186/1471-2105-13-255

[…] ontigs translocated. Coverage values are computed after the first iteration of co-linear chaining. The reference genome is Caenorhabditis Elegans of length 100.3 Mbp. The assembly was produced by the MIP Scaffolder of [] and has N50 value 189704.For the experiment we ran the validate_distributed.sh script of our tool with parameters maxerror 0.02, minlen 35, maxgap 5000 and numjobs 120. Here the t […]


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MIP Scaffolder institution(s)
Department of Computer Science, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland

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