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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


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Publication for MIP Scaffolder

MIP Scaffolder citations


Approaches for in silico finishing of microbial genome sequences

PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] 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 […]


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

PMCID: 4164777
PMID: 25189940
DOI: 10.1038/ncomms5737

[…] 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 […]


Normalized N50 assembly metric using gap restricted co linear chaining

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

[…] 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. […]

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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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