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|Alternative names||HSP base Assignment using NGS data through Diploid Similarity, HANDS2|
|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.|
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- person_outline Aziz Mithani
Publications for HSP base Assignment using NGS data through Diploid Similarity
Homeolog expression analysis in an allotriploid non model crop via integration of transcriptomics and proteomics
[…] 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
[…] How to cite this article: Khan, A. et al. HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data. Sci. Rep. 6, 29234; doi: 10.1038/srep29234 (2016). […]
Development of practice guidelines for hemodialysis in Egypt
[…] 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?
[…] 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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