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QIIME (English: / tʃ aɪ m / ch-eye-m) [1] is a bioinformatics data science platform, originally developed for analysis of high-throughput microbiome marker gene (e.g., 16S or 18S rRNA genes) amplicon sequencing data. There have been two major versions of the QIIME platform, QIIME 1 [2] and QIIME 2. [3]
It can map Illumina and SOLiD reads. Unlike most mapping programs, speed increases for longer read lengths. Yes Free, GPL [49] PRIMEX Indexes the genome with a k-mer lookup table with full sensitivity up to an adjustable number of mismatches. It is best for mapping 15-60 bp sequences to a genome. No No Yes No, multiple processes per search 2003
Generic Mapping Tools [16] Map generation and analysis Lamont–Doherty and University of Hawaii: GPL: Cross-platform: C: Implemented in OpendTect GPlates [17] Interactive visualization of plate tectonics University of Sydney, Caltech, NGU: GPL: Cross-platform: C++, Python: Implements GPML: OpenStereo [18] [19] Geoscience plotting tool
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4]
It uses the seed-and-vote mapping paradigm to determine the mapping location of the read by using its largest mappable region. It automatically decides whether the read should be globally mapped or locally mapped. For RNA-seq data, Subread should be used for the purpose of expression analysis. Subread can also be used to map DNA-seq reads.
"The Generic Mapping Tools". generic-mapping-tools.org. 2021-02-15 "planiglobe - online vector map creation". Kiel, Germany: kk+w - digitale kartografie GmbH. September 2, 2008. Archived from the original on February 4, 2012 Interactive online map generation using GMT. Phillips, Doug (September 11, 2003).
The product includes applications for read mapping, RNA-seq, ChIP-seq, and genomic variant analysis. [ 16 ] In October 2011, following news that the National Center for Biotechnology Information would phase out funding for its Sequence Read Archive (SRA), DNAnexus said it was working with Google Cloud Storage to host a mirror of the SRA database.
Concept mapping and mind mapping software is used to create diagrams of relationships between concepts, ideas, or other pieces of information. It has been suggested that the mind mapping technique can improve learning and study efficiency up to 15% over conventional note-taking . [ 1 ]