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MIP Scaffolder specifications


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


No version available

Publication for MIP Scaffolder

MIP Scaffolder citations


Approaches for in silico finishing of microbial genome sequences

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 […]


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

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. […]


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

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 […]


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

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 […]


ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

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 […]


Normalized N50 assembly metric using gap restricted co linear chaining

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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