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Protocols

DART specifications

Information


Unique identifier OMICS_20841
Name DART
Alternative name Division based Alignment for RNA-Seq Transcripts
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A BWT-based index file and takes a read library (single-end or paired-end reads).
Input format FASTA, FASTQ
Output data Read alignments.
Output format SAM
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1.2
Stability Stable
Maintained Yes

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Versioning


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Maintainers


  • person_outline Wen-Lian Hsu
  • person_outline Hsin-Nan Lin

Publication for Division based Alignment for RNA-Seq Transcripts

DART citations

 (4)
call_split

Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data

2018
R Soc Open Sci
PMCID: 5936904
PMID: 29765639
DOI: 10.1098/rsos.171615
call_split See protocol

[…] Skin samples were collected from spotted dolphins and spinner dolphins via biopsy dart [] on research cruises, from specimens taken as bycatch in the tuna purse-seine fishery, or from stranded or beachcast individuals. Biopsies were collected in accordance to the best practices of […]

library_books

DART: a fast and accurate RNA seq mapper with a partitioning strategy

2017
Bioinformatics
PMCID: 5860201
PMID: 28968831
DOI: 10.1093/bioinformatics/btx558

[…] ons (). Furthermore, some aligners might fail to detect splice junctions if sequencing errors happen at their neighboring locations. In this study, we proposed a novel RNA-Seq mapping algorithm, call DART (Division based Alignment for RNA-Seq Transcripts) to handle spliced alignment without any annotation guidance. It is derived from our DNA read mapper, Kart (). DART adopts a partitioning strateg […]

library_books

Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource

2015
Sci Rep
PMCID: 4655351
PMID: 26593698
DOI: 10.1038/srep16916

[…] DArTseq™ represents a combination of DArT complexity reduction methods and next generation sequencing platforms. This represents a new implementation of sequencing complexity reduced representations and more recent applications of this c […]

call_split

Dispersal Routes and Habitat Utilization of Juvenile Atlantic Bluefin Tuna, Thunnus thynnus, Tracked with Mini PSAT and Archival Tags

2012
PLoS One
PMCID: 3358288
PMID: 22629461
DOI: 10.1371/journal.pone.0037829
call_split See protocol

[…] and tether assemblies, materials and tagging procedures were similar to those previously described for adult ABFT , , with tether length adjusted for smaller fish. Tags were attached by inserting the dart near the base of the second dorsal fin. In 2007, we experimented with a secondary attachment to reduce tag movement during swimming (n = 16). This consisted of a short length of monofilament in a […]

Citations

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DART institution(s)
Institute of Information Science, Academia Sinica, Taipei, Taiwan
DART funding source(s)
Supported by Bioinformatics Core Facility for Translational Medicine and Biotechnology Development / MOST105-2319-B-400-002.

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