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Targeted Assembler of [short] Sequence Reads TASR

A genomics application that allows hypothesis-based interrogation of genomic regions (sequence targets) of interest. It only considers NGS reads for assembly that have overlap potential to input sequence targets.

Official website
Specifications
Publications
Classification

Specifications

Software type:: Package
Interface:: Command line interface
Restrictions to use:: None
Biological technology:: Illumina
Operating system:: Unix/Linux, Mac OS
Programming languages:: Perl
License:: GNU General Public License version 2.0
Computer skills:: Advanced
Stability:: Stable

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Publications

(Warren and Holt, 2011) Targeted assembly of short sequence reads. PloS one.
PMID: 21589938

Classification

Literature

(Magoc et al., 2013) GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics.
PMID: 23665771
(Miller et al., 2010) Assembly algorithms for next-generation sequencing data. Genomics.
PMID: 20211242
(Narzisi and Mishra, 2011) Comparing de novo genome assembly: the long and short of it. PloS one.
PMID: 21559467
(Henson et al., 2012) Next-generation sequencing and large genome assemblies. Pharmacogenomics.
PMID: 22676195
(Kleftogiannis et al., 2013) Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PloS one.
PMID: 24086547
(Nagarajan and Pop, 2013) Sequence assembly demystified. Nature reviews Genetics.
PMID: 23358380
(Bradnam et al., 2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience.
PMID: 23870653
(Salzberg et al., 2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome research.
PMID: 22147368
(Utturkar et al., 2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics.
PMID: 24930142
(Alkan et al., 2011) Limitations of next-generation genome sequence assembly. Nature methods.
PMID: 21102452
(Love et al., 2016) Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC genomics.
PMID: 26944054

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