TULIP protocols

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TULIP specifications

Information


Unique identifier OMICS_16747
Name TULIP
Alternative name The Uncorrected Long-read Integration Process
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Michael Liem <>

Publication for The Uncorrected Long-read Integration Process

TULIP in pipelines

 (2)
2017
PMCID: 5543108
PMID: 28775309
DOI: 10.1038/s41598-017-07650-6

[…] be chosen to facilitate further sequence integration. if a high density genetic map is available for a species, map markers could serve as pre-ordered seeds. for example, with minor modifications, tulip might be used to selectively add long read sequencing data only to single map marker bins (containing thousands of actual, unordered markers) resulting from a population sequencing strategy., […]

2017
PMCID: 5543108
PMID: 28775309
DOI: 10.1038/s41598-017-07650-6

[…] of alignments). with all other settings as before, this yielded the following parameters: -k 14 -w 45 (r7.3 2d); -k 16 -w 50 (r9 1d); -k 19 -w 60 (r9 2d); -k 16 -w 60 (r9.4 1d)., currently, tulip consists of two prototype scripts in perl: tulipseed.perl and tulipbulb.perl (version 0.4 ‘european eel’). the tulipseed script constructs the seed graph based on input sam files and a set seed […]


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TULIP in publication

PMCID: 5543108
PMID: 28775309
DOI: 10.1038/s41598-017-07650-6

[…] genome dozens of gigabases long would require several years on a cluster., we are currently developing a computational pipeline specifically intended for future sequencing of extremely large tulip genomes (up to 35 gbp). named tulip (for the uncorrected long-read integration process), its primary purpose is to split up such large assembly problems into manageable subsets of long reads. […]


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TULIP institution(s)
ZF-screens B.V., Leiden, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands; Muséum National d’Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, UCN, UA, Paris, France; Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Basic Science and Aquatic Medicine, Oslo, Norway; DUPAN, Wageningen, The Netherlands; Animal Breeding and Genomics Centre, Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands; Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria; University of Applied Sciences Leiden, Leiden, The Netherlands; Generade Centre of Expertise in Genomics, Leiden, The Netherlands
TULIP funding source(s)
This project was funded by grants from the DUPAN Foundation for sustainable eel farming and fishing, the Dutch Ministry of Economic Affairs (KB-21-001-001), the Austrian Science Foundation (P26363-B25), the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Actions: Innovative Training Network IMPRESS, grant agreement No 642893 and by local funds from CNRS and Generade, the Leiden Centre of Expertise in Genomics.

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