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shenwei356 · Aug 5, 2024 · 0b80e1e · 0b80e1e
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diff --git a/faqs/index.html b/faqs/index.html
@@ -1449,7 +1449,7 @@ <h1>FAQs</h1>
 </code></pre><p>Maximum genome size is about 268 Mb (268,435,456). More precisely:</p>
 <pre><code>$total_bases + ($num_contigs - 1) * 1000 &lt;= 268,435,456
 </code></pre>
-<p>as we insert 1000-bp intervals of N’s between contigs to reduce the sequence scale to index.</p>
+<p>as we concatenate contigs with 1000-bp intervals of N’s to reduce the sequence scale to index.</p>
 <p>For big and complex genomes, like the human genome (chr1 is ~248 Mb) which has many repetitive sequences, LexicMap would be slow to align.</p>
 <div class="flex align-center gdoc-page__anchorwrap">
     <h3 id="hows-the-hardware-requirement"

diff --git a/installation/index.html b/installation/index.html
@@ -77,7 +77,7 @@
       "url" : "https://bioinf.shenwei.me/LexicMap/installation/",
       "headline": "Installation",
       "description": "LexicMap can be installed via conda, executable binary files, or compiling from the source.\nBesides, it supports shell completion, which could help accelerate typing.\nConda Install conda, then run\nconda install -c bioconda lexicmap Linux and MacOS (both x86 and arm CPUs) are supported.\nBinary files Linux Download the binary file.\nOS Arch File, 中国镜像 Linux 64-bit lexicmap_linux_amd64.tar.gz, 中国镜像 Linux arm64 lexicmap_linux_arm64.tar.gz, 中国镜像 Decompress it:\ntar -zxvf lexicmap_linux_amd64.tar.gz If you have the root privilege, simply copy it to \/usr\/local\/bin:",
-      "wordCount" : "339",
+      "wordCount" : "443",
       "inLanguage": "en",
       "isFamilyFriendly": "true",
       "mainEntityOfPage": {
@@ -1528,9 +1528,20 @@ <h1>Installation</h1>
 <p>If you have the root privilege, simply copy it to <code>/usr/local/bin</code>:</p>
 <pre><code> sudo cp lexicmap /usr/local/bin/
 </code></pre>
-<p>Or copy to anywhere in the environment variable <code>PATH</code>:</p>
+</li>
+<li>
+<p>If you don&rsquo;t have the root privilege, copy it to any directory in the environment variable <code>PATH</code>:</p>
 <pre><code> mkdir -p $HOME/bin/; cp lexicmap $HOME/bin/
 </code></pre>
+<p>And optionally add the directory into the environment variable <code>PATH</code> if it&rsquo;s not in.</p>
+<pre><code> # bash
+ echo export PATH=\$PATH:\$HOME/bin/ &gt;&gt; $HOME/.bashrc
+ source $HOME/.bash # apply the configuration
+
+ # zsh
+ echo export PATH=\$PATH:\$HOME/bin/ &gt;&gt; $HOME/.zshrc
+ source $HOME/.zshrc # apply the configuration
+</code></pre>
 </li>
 </ol>
 
@@ -1547,7 +1558,8 @@ <h1>Installation</h1>
     </label>
     <div class="gdoc-markdown--nested gdoc-tabs__content">
       <ol>
-<li>Download the binary file.
+<li>
+<p>Download the binary file.</p>
 <div class="table-wrap"> <table>
 <thead>
 <tr>
@@ -1582,6 +1594,20 @@ <h1>Installation</h1>
 </tbody>
 </table> </div>
 </li>
+<li>
+<p>Copy it to any directory in the environment variable <code>PATH</code>:</p>
+<pre><code> mkdir -p $HOME/bin/; cp lexicmap $HOME/bin/
+</code></pre>
+<p>And optionally add the directory into the environment variable <code>PATH</code> if it&rsquo;s not in.</p>
+<pre><code> # bash
+ echo export PATH=\$PATH:\$HOME/bin/ &gt;&gt; $HOME/.bashrc
+ source $HOME/.bash # apply the configuration
+
+ # zsh
+ echo export PATH=\$PATH:\$HOME/bin/ &gt;&gt; $HOME/.zshrc
+ source $HOME/.zshrc # apply the configuration
+</code></pre>
+</li>
 </ol>
 
     </div>

diff --git a/search/en.data.min.json b/search/en.data.min.json
diff --git a/tutorials/index/index.html b/tutorials/index/index.html
@@ -1504,7 +1504,7 @@ <h1>Building an index</h1>
 More precisely:</p>
 <pre><code>$total_bases + ($num_contigs - 1) * 1000 &lt;= 268,435,456
 </code></pre>
-<p>as we insert 1000-bp intervals of N&rsquo;s between contigs to reduce the sequence scale to index.</p>
+<p>as we concatenate contigs with 1000-bp intervals of N’s to reduce the sequence scale to index.</p>
 </div>
 </blockquote>
 

diff --git a/usage/index/index.html b/usage/index/index.html
@@ -59,7 +59,7 @@
       "url" : "https://bioinf.shenwei.me/LexicMap/usage/index/",
       "headline": "index",
       "description": "$ lexicmap index -h Generate an index from FASTA\/Q sequences Input: *1. Sequences of each reference genome should be saved in separate FASTA\/Q files, with reference identifiers in the file names. 2. Input plain or gzip\/xz\/zstd\/bzip2 compressed FASTA\/Q files can be given via positional arguments or the flag -X\/--infile-list with a list of input files. Flag -S\/--skip-file-check is optional for skipping file checking if you trust the file list. 3. Input can also be a directory containing sequence files via the flag -I\/--in-dir, with multiple-level sub-directories allowed.",
-      "wordCount" : "1246",
+      "wordCount" : "1278",
       "inLanguage": "en",
       "isFamilyFriendly": "true",
       "mainEntityOfPage": {
@@ -1434,8 +1434,8 @@ <h1>index</h1>
 </span></span><span class="line"><span class="cl">     (-G/--big-genomes).
 </span></span><span class="line"><span class="cl">     You need to increase the value for indexing fungi genomes.
 </span></span><span class="line"><span class="cl">  5. Maximum genome size: 268,435,456.
-</span></span><span class="line"><span class="cl">     More precisely: $total_bases + ($num_contigs - 1) * 1000 &lt;= 268,435,456, as we insert 1000-bp intervals
-</span></span><span class="line"><span class="cl">     of N&#39;s between contigs to reduce the sequence scale to index.
+</span></span><span class="line"><span class="cl">     More precisely: $total_bases + ($num_contigs - 1) * 1000 &lt;= 268,435,456, as we concatenate contigs with
+</span></span><span class="line"><span class="cl">     1000-bp intervals of N’s to reduce the sequence scale to index.
 </span></span><span class="line"><span class="cl">
 </span></span><span class="line"><span class="cl">  Attention:
 </span></span><span class="line"><span class="cl">   *1) ► You can rename the sequence files for convenience, e.g., GCF_000017205.1.fa.gz, because the genome
@@ -1518,9 +1518,12 @@ <h1>index</h1>
 </span></span><span class="line"><span class="cl">Flags:
 </span></span><span class="line"><span class="cl">  -b, --batch-size int            ► Maximum number of genomes in each batch (maximum value: 131072)
 </span></span><span class="line"><span class="cl">                                  (default 5000)
-</span></span><span class="line"><span class="cl">  -G, --big-genomes string        ► Out file of skipped files with genomes &gt;= -g/--max-genome
+</span></span><span class="line"><span class="cl">  -G, --big-genomes string        ► Out file of skipped files with $total_bases + ($num_contigs - 1) *
+</span></span><span class="line"><span class="cl">                                  $contig_interval &gt;= -g/--max-genome. The second column is one of the
+</span></span><span class="line"><span class="cl">                                  skip types: no_valid_seqs, too_large_genome, too_many_seqs.
 </span></span><span class="line"><span class="cl">  -c, --chunks int                ► Number of chunks for storing seeds (k-mer-value data) files.
 </span></span><span class="line"><span class="cl">                                  (default 16)
+</span></span><span class="line"><span class="cl">      --contig-interval int       ► Length of interval (N&#39;s) between contigs in a genome. (default 1000)
 </span></span><span class="line"><span class="cl">  -r, --file-regexp string        ► Regular expression for matching sequence files in -I/--in-dir,
 </span></span><span class="line"><span class="cl">                                  case ignored. (default
 </span></span><span class="line"><span class="cl">                                  &#34;\\.(f[aq](st[aq])?|fna)(\\.gz|\\.xz|\\.zst|\\.bz2)?$&#34;)