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HANDS specifications


Unique identifier OMICS_22633
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




No version available


  • person_outline Aziz Mithani

Additional information


Publications for HSP base Assignment using NGS data through Diploid Similarity

HANDS citations


Homeolog expression analysis in an allotriploid non model crop via integration of transcriptomics and proteomics

Sci Rep
PMCID: 5777989
PMID: 29358676
DOI: 10.1038/s41598-018-19684-5

[…] ity 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 the ref […]


HANDS2: accurate assignment of homoeallelic base identity in allopolyploids despite missing data

Sci Rep
PMCID: 4932600
PMID: 27378447
DOI: 10.1038/srep29234

[…] We tested the accuracy of base assignments made by HANDS2 using the high-throughput RNA sequencing (RNA-seq) data for hexaploid bread wheat (T. aestivum; AABBDD) and its diploid-progenitors (Triticum urartu; AA, Aegilops speltoides; BB, and Aegilops t […]


Development of practice guidelines for hemodialysis in Egypt

PMCID: 3008948
PMID: 21206681
DOI: 10.4103/0971-4065.73450

[…] minArterial and venous pressure limitsColor of blood and dialyserBlood lines and circuit integrityTemperature: Pre- and postdialysis and when neededTermination of dialysisGather all supplies2.1. Wash hands2.2. Wear glovesStart and termination:1. Reset the arterial and venous monitor gauges to wider limits2. Stop the blood pump3. Clamp the arterial needle line4. Clamp the arterial machine lines5. T […]


Acute onset polyarthritis in older people: Is it RS3PE syndrome?

PMCID: 2543002
PMID: 18759976
DOI: 10.1186/1757-1626-1-132

[…] me in a series of 10 patients. Following a retrospective multicenter study of patients Olive et al. [] proposed the following diagnostic criteria for this syndrome:1. Bilateral pitting oedema of both hands2. Sudden onset of polyarthritis3. Age more than 50 years4. Seronegative rheumatoid factor.The exact incidence and prevalence are not known. RS3PE affects more men than women with ratio of 2:1 an […]

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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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