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    生物信息分析
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    • A
      anneng 最后由 编辑

      http://ccb.jhu.edu/software/choosing-a-metagenomics-classifier/
      How to Choose Your Metagenomics Classification Tool

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      • A
        anneng 最后由 anneng 编辑

        https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13095
        Identification of the taxonomic origin of a DNA sequence is crucial for many sequencing projects, e.g. metagenomics studies, identification of contaminations in whole genome sequencing projects and filtering of organisms of interest in marker‐gene based community analyses.
        Last common ancestor algorithms are powerful approaches to estimate the taxonomy of a given sequence and have been widely used for classification of next‐generation sequencing (NGS) reads, also known as 2nd generation sequencing reads.
        Here, we present BASTA (https://github.com/timkahlke/BASTA), a basic sequence taxonomy annotator, which extends last common ancestor estimations from sequencing reads to any kind of nucleotide or amino acid sequence utilizing NCBI taxonomies of user‐defined best hits.
        BASTA can be configured to use the output of many common sequence comparison tools, e.g. BLAST and Diamond, in conjunction with either provided or user‐defined target sequence databases.
        6253df26-2c42-4a10-bfb1-c34e1f1e1da2-image.png

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        • A
          anneng 最后由 编辑

          https://webcache.googleusercontent.com/search?q=cache:fJfbDasHie8J:https://nickilottmetagenomics.wordpress.com/2015/01/19/comparing-diamond-lca-against-kraken/+&cd=10&hl=en&ct=clnk&gl=us
          DIAMOND + LCA outperforms Kraken in the sensitivity stakes by ~10 fold when assigning reads from mouse gut to genera. Accuracy of these assignments is not assessed, however.
          DIAMOND+LCA

          DIAMOND (version 0.3.9) was run using the following command:

          diamond blastx –db /ifs/mirror/diamond/nr –query <input.fastq> -v 2 –threads 16 -o <diamond.output.tsv>

          LCA mapper (from mtools, MEGAN5) was run using:

          lcamapper.sh -i <diamond.output.tsv> -f Detect -ms 50 -me 0.01 -tp 50 -gt megan/gi_taxid_prot.bin -o <lca.output>

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          • A
            anneng 最后由 编辑

            https://jshleap.github.io/bioinformatics/writting-jMEGAN_notes/
            Introduction to MEGAN methods

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            • A
              anneng 最后由 编辑

              NCBI taxonomy databases
              https://www.uppmax.uu.se/resurser/databases/ncbi-taxonomy-databases/
              Name Source Notes
              taxdump NCBI NCBI taxonomic database, in multiple .dmp files (see taxdump_readme.txt or link)
              taxcat NCBI NCBI taxonomic categories, in categories.dmp (see taxcat_readme.txt or link)
              taxdump_readme.txt NCBI NCBI taxdump file description
              taxcat_readme.txt NCBI NCBI taxcat file description
              gi_taxid_nucl.dmp NCBI Mappings of nucleotide GI to taxid (DEPRECATED)
              gi_taxid_prot.dmp NCBI Mappings of protein GI to taxid (DEPRECATED)
              nucl_wgs.accession2taxid NCBI TaxID mapping for nucleotide records of type WGS or TSA
              nucl_gb.accession2taxid NCBI TaxID mapping for nucleotide records not of the above types
              prot.accession2taxid NCBI TaxID mapping for protein records
              pdb.accession2taxid NCBI TaxID mapping for PDB protein records
              dead_nucl.accession2taxid NCBI TaxID mapping for dead nucleotide records
              dead_prot.accession2taxid NCBI TaxID mapping for dead protein records
              dead_wgs.accession2taxid NCBI TaxID mapping for dead WGS or TSA records

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              • A
                anneng 最后由 anneng 编辑

                http://currents.plos.org/treeoflife/index.html%3Fp=395.html
                将NCBI和wiki联系起来

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                • A
                  anneng 最后由 编辑

                  http://ccb.jhu.edu/software/choosing-a-metagenomics-classifier/

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                  • A
                    anneng 最后由 编辑

                    https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC5978398/
                    BLAST-based validation of metagenomic sequence assignments
                    用blast对宏基因的序列物种鉴定（例如kraken）进行校正

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                    • A
                      anneng 最后由 编辑

                      Current Protocols - 2021 - Ba c - DIAMOND MEGAN Fast and Easy Taxonomic and Functional Analysis of Short and Long.pdf

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                      • A
                        anneng 最后由 编辑

                        https://www.future-science.com/doi/10.2144/000114135
                        TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences
                        这个里面提到 16S是人体微生物的进标准 物种注释大部分用RDP数据库分类 但是RDP少了NT中的很多参考序列 因此可以用TUIT做进一步的补充分类。TUIT也可以适用于其他场景。
                        TUIT 不限于任何特定类型的序列，并且对短至 125 个碱基对的序列保持高特异性水平；它还具有将序列分类到物种级别的能力。
                        f382dca4-d373-4f4e-a294-d1e287930f1a-image.png
                        b422e648-3f1a-4b30-9120-52ae4a6f6ea6-image.png

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                        • A
                          anneng 最后由 编辑

                          https://academic.oup.com/bib/article/19/3/495/2733162
                          Comparing genome versus proteome-based identification of clinical bacterial isolates
                          55e6d3da-3479-42f9-958d-002a12de02df-image.png

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