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custom_databases/index.html

@@ -154,7 +154,7 @@ <h2 id="non-standardcustom-accessions">Non-standard/custom accessions<a class="h
 </div>
 <div class="admonition warning">
 <p class="admonition-title">Warning</p>
-<p>the target and specialization fields (2nd and 4th col) cannot be the same as the target (3rd col)</p>
+<p>the target and specialization fields (2nd and 4th col) cannot be the same as the node (3rd col)</p>
 </div>
 <details>
   <summary>Examples of --input-file</summary>
@@ -252,20 +252,27 @@ <h3 id="plasmid-plastid-and-mitochondrion-from-refseq">Plasmid, Plastid and Mito
 wget -A genomic.fna.gz -m -nd --quiet --show-progress &quot;ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plastid/&quot;
 wget -A genomic.fna.gz -m -nd --quiet --show-progress &quot;ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/mitochondrion/&quot;
 
+# Split sequences in files and retrieve taxonomy
+mkdir sequences/
+zcat plasmid.* plastid.* mitochondrion.* | awk '$0 ~ &quot;&gt;&quot; {accver=(substr($1,2)); print accver}{print $0 &gt; &quot;sequences/&quot;accver&quot;.fna&quot;}' | ganon-get-seq-info.sh -e -i - | awk '{print &quot;sequences/&quot;$1&quot;.fna\t&quot;$1&quot;\t&quot;$3}' &gt; ppm.tsv
+
 # Build ganon database
-ganon build-custom --input plasmid.* plastid.* mitochondrion.* --db-prefix ppm --input-target sequence --level leaves --threads 32 
+ganon build-custom --input-file ppm.tsv --db-prefix ppm --level species --threads 16
+
+# OPTIONAL Remove temporary folder and downloaded files
+rm -rf sequences/ ppm.tsv plasmid.* plastid.* mitochondrion.* 
 </code></pre>
 <h3 id="univec-univec_core">UniVec, UniVec_core<a class="headerlink" href="#univec-univec_core" title="Permanent link">:)</a></h3>
 <p>"UniVec is a non-redundant database of sequences commonly attached to cDNA or genomic DNA during the cloning process." <a href="https://ftp.ncbi.nlm.nih.gov/pub/UniVec/README.uv">Website</a>. Useful to screen for vector and linker/adapter contamination. UniVec_core is a sub-set of the UniVec selected to reduce the false positive hits from real biological sources.</p>
 <pre><code class="language-bash"># UniVec
 wget -O &quot;UniVec.fasta&quot; --quiet --show-progress &quot;ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/UniVec&quot; 
-grep -o '^&gt;[^ ]*' UniVec.fasta | sed 's/^&gt;//' | awk '{print &quot;UniVec.fasta\t&quot;$1&quot;\t81077&quot;}' &gt; UniVec_ganon_input_file.tsv
-ganon build-custom --input-file UniVec_ganon_input_file.tsv --db-prefix UniVec --input-target sequence --level leaves --threads 8
+echo -e &quot;UniVec.fasta\tUniVec\t81077&quot; &gt; UniVec_Core_ganon_input_file.tsv
+ganon build-custom --input-file UniVec_ganon_input_file.tsv --db-prefix UniVec --level leaves --threads 8
 
 # UniVec_Core
 wget -O &quot;UniVec_Core.fasta&quot; --quiet --show-progress &quot;ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/UniVec_Core&quot; 
-grep -o '^&gt;[^ ]*' UniVec_Core.fasta | sed 's/^&gt;//' | awk '{print &quot;UniVec_Core.fasta\t&quot;$1&quot;\t81077&quot;}' &gt; UniVec_Core_ganon_input_file.tsv
-ganon build-custom --input-file UniVec_Core_ganon_input_file.tsv --db-prefix UniVec_Core --input-target sequence --level leaves --threads 8
+echo -e &quot;UniVec_Core.fasta\tUniVec_Core\t81077&quot; &gt; UniVec_Core_ganon_input_file.tsv
+ganon build-custom --input-file UniVec_Core_ganon_input_file.tsv --db-prefix UniVec_Core --level leaves --threads 8
 </code></pre>
 <div class="admonition note">
 <p class="admonition-title">Note</p>

index.html

@@ -133,6 +133,7 @@
                 <h1 id="ganon">ganon <a href="https://github.com/pirovc/ganon"><img alt="GitHub release (latest by date)" src="https://img.shields.io/github/v/release/pirovc/ganon" /></a><a class="headerlink" href="#ganon" title="Permanent link">:)</a></h1>
 <p><a href="https://travis-ci.com/pirovc/ganon"><img alt="Build Status" src="https://travis-ci.com/pirovc/ganon.svg?branch=master" /></a> <a href="https://codecov.io/gh/pirovc/ganon"><img alt="codecov" src="https://codecov.io/gh/pirovc/ganon/branch/master/graph/badge.svg" /></a> <a href="https://anaconda.org/bioconda/ganon"><img alt="Anaconda-Server Badge" src="https://anaconda.org/bioconda/ganon/badges/downloads.svg" /></a> <a href="https://anaconda.org/bioconda/ganon"><img alt="Anaconda-Server Badge" src="https://anaconda.org/bioconda/ganon/badges/platforms.svg" /></a> <a href="http://bioconda.github.io/recipes/ganon/README.html"><img alt="install with bioconda" src="https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat" /></a> <a href="https://dx.doi.org/10.1093/bioinformatics/btaa458"><img alt="Publication" src="https://img.shields.io/badge/DOI-10.1101%2F406017-blue" /></a> </p>
 <p>Code: <a href="https://github.com/pirovc/ganon">GitHub repository</a></p>
+<p><a href="https://www.biorxiv.org/content/10.1101/2023.12.07.570547">ganon2 pre-print</a></p>
 <p>ganon is designed to index large sets of genomic reference sequences and to classify reads against them efficiently. The tool uses <a href="https://doi.org/10.1186/s13059-023-02971-4">Hierarchical Interleaved Bloom Filters</a> as indices based on k-mers with optional minimizers. It was mainly developed, but not limited, to the metagenomics classification problem: quickly assign sequence fragments to their closest reference among thousands of references. After classification, taxonomic or sequence abundances are estimated and reported.</p>
 <h2 id="features">Features<a class="headerlink" href="#features" title="Permanent link">:)</a></h2>
 <ul>
@@ -764,5 +765,5 @@ <h2 id="parameters">Parameters<a class="headerlink" href="#parameters" title="Pe
 
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