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HANDS specifications

Information


Unique identifier OMICS_22633
Name HANDS
Alternative names HSP base Assignment using NGS data through Diploid Similarity, HANDS2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Files with the polyploid, file containing start and end coordinates for each gene/contig, files containing lists of HSPs and single base substitutions (SBSs) present in the polyploid and the diploid-progenitors respectively and base coverage files containing number of reads supporting a particular base.
Input format SAM/BAM+GFF+VCF
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Aziz Mithani <>

Additional information


https://genomics.lums.edu.pk/software/hands/

Publications for HSP base Assignment using NGS data through Diploid Similarity

HANDS in publications

 (2)
PMCID: 5777989
PMID: 29358676
DOI: 10.1038/s41598-018-19684-5

[…] greatly increases computational effort, hampering quantitative results per genome. consequently the rna reads are not separated and traced back to their (sub-) genome. algorithms like polycat and hands2 process reads based on classification towards their genome of origin, but heavily depend on the presence and the quality of reference genomes,. since not all cultivars of interest carry […]

PMCID: 5636024
DOI: 10.15256/joc.2015.5.52

[…] trajectories of number processing and calculation. developmental neuropsychology, 36(6), 763–87., keywords: fmri; parietal; frontal; cognition; saccades; mathematic; numerical; dcd., t. grace1, b. hands2, m. bulsara2 & c. pennell3, 1institute for health research, the university of notre dame australia, fremantle, 6959, australia. [email protected]; 2institute for health research, […]


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HANDS institution(s)
Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), D.H.A., Lahore, Pakistan; Department of Plant Sciences, University of Oxford, Oxford, UK
HANDS funding source(s)
Supported by LUMS Faculty Start-up Grant.

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