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Merge pull request #6 from mantczakaus/patch-3
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Update if89.md
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ziadbkh authored Apr 5, 2024
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Expand Up @@ -133,6 +133,15 @@ A list of the currently available (`as of 25 Jan 2023`) databases is included be
traditional divisions of GenBank, EMBL, and DDBJ.
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<td>Blast</td>
<td><a href="https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html"> Blast Webpage </a></td>
<td> 7 Nov 2023 </td>
<td><code>blast_db/07112023</code></td>
<td><strong>nt.*</strong>: nucleotide sequence database, with entries from all
traditional divisions of GenBank, EMBL, and DDBJ.
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<td>Alphafold/UniProt</td>
<td> <a href="https://github.com/steineggerlab/foldseek"> foldseek github pages</a> and <a href="https://alphafold.ebi.ac.uk/"> AlphaFold Protein Structure Database webpage </a></td>
Expand Down Expand Up @@ -175,6 +184,22 @@ A list of the currently available (`as of 25 Jan 2023`) databases is included be
<td><code>busco_db/14082023/lineages</code></td>
<td>Lineage datasets for busco tool. Downloaded manually.</td>
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<td>Kaiju</td>
<td><a href="https://bioinformatics-centre.github.io/kaiju/downloads.html"> Kaiju Webpage </a></td>
<td> 26 May 2023 </td>
<td><code>kaiju/26052023/kaiju_db_rvdb</code></td>
<td>Kaiju pre-built indexes for protein sequences from RVDB-prot v26.0. Contains the Kaiju .fmi index file, as well as nodes.dmp and names.dmp from the NCBI taxonomy.
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<td>Kraken2</td>
<td><a href="https://benlangmead.github.io/aws-indexes/k2"> Kraken 2, KrakenUniq and Bracken indexes </a></td>
<td> 9 Oct 2023 </td>
<td><code>kraken2/09102023/k2_pluspf</code></td>
<td>Kraken2 pre-built index for RefSeq database (archaea, bacteria, viral, plasmid, human, protozoa & fungi) plus UniVec_Core.
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</table>
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