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MOESM2 of HIA: a genome mapper using hybrid index-based sequence alignment

Jongpill Choi, Kiejung Park, Seong Cho, Myungguen Chung
2016 Figshare  
It contains the jar file of HIA. HIA can be used without restriction.  ...  Illumina-like 100 bp (single-end) dataset indexing time of HIA is comparable to other aligners. Especially, HIA is able to reduce the time of index generation by using multiple threads.  ...  We summarize the parameters used in the tests as follows: Aligner Options Description Time measurement is elapsed time (minute). Memory is the peak memory for the index construction.  ... 
doi:10.6084/m9.figshare.c.3608045_d1 fatcat:spx4jpuprzd2vpczrzhr3ifc4y

HIA: a genome mapper using hybrid index-based sequence alignment

Jongpill Choi, Kiejung Park, Seong Beom Cho, Myungguen Chung
2015 Algorithms for Molecular Biology  
Results: HIA uses two indices, a hash table index and a suffix array index.  ...  The hybrid index is used to find candidate alignment regions (CARs) between a reference and a read.  ...  To this end, we developed a genome mapper using hybrid index-based sequence alignment (HIA).  ... 
doi:10.1186/s13015-015-0062-4 pmid:26702294 pmcid:PMC4688996 fatcat:iyrr2umxbzf2vgbbwijchdosw4

Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
2016 Zenodo  
We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters.  ...  An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion.  ...  Hybrid-index based mappers, HIA [288] and YOABS [289] , combine both hash tables and a BWT-based indexes. Mappers Slider II [290] and Slider [291] use merge sorting.  ... 
doi:10.5281/zenodo.1045317 fatcat:agbwpocisncwvihn2ij5q3ongq

Diet outweighs genetics in shaping gut microbiomes in Asian honeybee [article]

Qinzhi Su, Min Tang, Jiahui Hu, Junbo Tang, Xue Zhang, Xingan Li, Qingsheng Niu, Xuguo Zhou, Shiqi Luo, Xin Zhou
2022 bioRxiv   pre-print
The gut microbiome is a crucial element that facilitates a host adaptation to a changing environment.  ...  Bacterial composition varied significantly across populations at phylotype, sequence-discrete population (SDP), and strain levels, but with extensive overlaps, indicating the diversity of microbial community  ...  Chenyi Li, Yating Du, Chengfeng Yang, Lizhen Guo, Lifei Qiu and Wenjun from China Agricultural University isolated and cultured honeybee gut bacteria that were for genome sequencing in this work.  ... 
doi:10.1101/2022.01.23.477436 fatcat:vr6v47b4sfcgvdp53ktcirusjm

Knowledge Extracted from Copernicus Satellite Data

Dumitru Octavian, Schwarz Gottfried, Eltoft Torbjørn, Kræmer Thomas, Wagner Penelope, Hughes Nick, Arthus David, Fleming Andrew, Koubarakis Manolis, Datcu Mihai
2019 Zenodo  
By applying an already established active learning approach based on a Support Vector Machine with relevance feedback [2], we can limit ourselves to a limited number of typical satellite images to extract  ...  This approach is also a simple way to generate benchmarking datasets that can be used for testing and validating different algorithms, and for creating additional bigger datasets for large-scale demonstrations  ...  Automatic glaciers lake mapping, normalized different water index and modify normalized water difference index with on screen digitization (1, 2).  ... 
doi:10.5281/zenodo.3941573 fatcat:zzifwgljifck5bpjnboetsftfu