From 3f2bab77c87c2cfda360c2294d08ff0c060582e2 Mon Sep 17 00:00:00 2001
From: mantczakaus <49752271+mantczakaus@users.noreply.github.com>
Date: Mon, 18 Mar 2024 14:39:50 +1000
Subject: [PATCH] Update if89.md

Added new blastdb, kaiju and kraken2
---
 if89.md | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/if89.md b/if89.md
index b4dc14a..08fcb02 100755
--- a/if89.md
+++ b/if89.md
@@ -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.
                   </td>
                 </tr>
+                <tr>
+                   <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.
+                   </td>
+                </tr>
                 <tr>
                   <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>
@@ -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>
                 </tr>
+                <tr>
+                 <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.
+                 </td>
+               </tr>
+               <tr>
+                 <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.
+                 </td>
+               </tr>
               </tbody>
             </table>
           </div>