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‎introduction/index.html

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@@ -1482,15 +1482,15 @@ <h1>Introduction</h1>
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class="gdoc-markdown__link"
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href="https://bioinf.shenwei.me/LexicMap/introduction/#searching"
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>fast and memory-efficient</a></strong>.</li>
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<li>LexicMap is easy to <a
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<li>LexicMap is <strong>easy to <a
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class="gdoc-markdown__link"
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href="http://bioinf.shenwei.me/LexicMap/installation/"
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>install</a>,
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>install</a></strong>,
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we provide <a
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class="gdoc-markdown__link"
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href="https://github.com/shenwei356/LexicMap/releases/"
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>binary files</a> with no dependencies for Linux, Windows, MacOS (x86 and arm CPUs).</li>
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<li>LexicMap is easy to use (<a
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<li>LexicMap is <strong>easy to use</strong> (<a
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class="gdoc-markdown__link"
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href="http://bioinf.shenwei.me/LexicMap/tutorials/index/"
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>tutorials</a> and <a
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<li><strong>We added the support of suffix matching of seeds, making seeds much more tolerant to mutations</strong>. Any 31-bp seed with a common ≥15 bp prefix or suffix can be matched, which means <strong>seeds are immune to any single SNP</strong>.</li>
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</ol>
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</li>
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<li>A multi-level index enables fast and low-memory variable-length seed matching and chaining.</li>
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<li>A hierarchical index enables fast and low-memory variable-length seed matching and chaining.</li>
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<li>A pseudo alignment algorithm is used to find similar sequence regions from chaining results for alignment.</li>
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<li>A <a
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class="gdoc-markdown__link"
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<tr>
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<td style="text-align:left">GTDB complete</td>
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<td style="text-align:right">402,538</td>
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<td style="text-align:right">578 GB</td>
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<td style="text-align:right">443 GB</td>
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<td style="text-align:left">LexicMap</td>
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<td style="text-align:right">906 GB</td>
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<td style="text-align:right">973 GB</td>
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<td style="text-align:right">10 h 36 m</td>
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<td style="text-align:right">63.3 GB</td>
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</tr>
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<td style="text-align:right"></td>
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<td style="text-align:right"></td>
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<td style="text-align:left">Blastn</td>
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<td style="text-align:right">360 GB</td>
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<td style="text-align:right">387 GB</td>
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<td style="text-align:right">3 h 11 m</td>
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<td style="text-align:right">718 MB</td>
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</tr>
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<tr>
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<td style="text-align:left">AllTheBacteria HQ</td>
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<td style="text-align:right">1,858,610</td>
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<td style="text-align:right">3.1 TB</td>
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<td style="text-align:right">2.5 TB</td>
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<td style="text-align:left">LexicMap</td>
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<td style="text-align:right">3.88 TB</td>
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<td style="text-align:right">4.26 TB</td>
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<td style="text-align:right">48 h 08 m</td>
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<td style="text-align:right">88.6 GB</td>
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</tr>
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<td style="text-align:right"></td>
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<td style="text-align:right"></td>
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<td style="text-align:left">Blastn</td>
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<td style="text-align:right">1.76 TB</td>
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<td style="text-align:right">1.93 TB</td>
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<td style="text-align:right">14 h 03 m</td>
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<td style="text-align:right">2.9 GB</td>
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</tr>
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<tr>
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<td style="text-align:left">Genbank+RefSeq</td>
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<td style="text-align:right">2,340,672</td>
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<td style="text-align:right">3.5 TB</td>
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<td style="text-align:right">2.7 TB</td>
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<td style="text-align:left">LexicMap</td>
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<td style="text-align:right">4.94 TB</td>
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<td style="text-align:right">5.43 TB</td>
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<td style="text-align:right">54 h 33 m</td>
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<td style="text-align:right">178.3 GB</td>
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</tr>
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<td style="text-align:right"></td>
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<td style="text-align:right"></td>
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<td style="text-align:left">Blastn</td>
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<td style="text-align:right">2.15 TB</td>
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<td style="text-align:right">2.37 TB</td>
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<td style="text-align:right">14 h 04 m</td>
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<td style="text-align:right">4.3 GB</td>
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</tr>
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<td style="text-align:left">LexicMap</td>
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<td style="text-align:right">3,867,003</td>
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<td style="text-align:right">2,228,339</td>
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<td style="text-align:right">1,165 s</td>
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<td style="text-align:right">20.2 GB</td>
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<td style="text-align:right">1,254 s</td>
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<td style="text-align:right">21.4 GB</td>
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</tr>
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<tr>
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<td style="text-align:left"></td>

‎search/en.data.min.json

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‎tutorials/index/index.html

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"url" : "https://bioinf.shenwei.me/LexicMap/tutorials/index/",
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"headline": "Step 1. Building a database",
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"description": "Table of contents Table of contents TL;DR Input Hardware requirements Algorithm Parameters Steps Output File structure Index size Explore the index TL;DR Prepare input files: Sequences of each reference genome should be saved in separate FASTA\/Q files, with identifiers in the file names. E.g., GCF_000006945.2.fna.gz While if you save a few small (viral) complete genomes (one sequence per genome) in each file, it’s feasible as sequence IDs in search result can help to distinguish targe genomes.",
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"wordCount" : "2840",
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"wordCount" : "2851",
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"inLanguage": "en",
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"isFamilyFriendly": "true",
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"mainEntityOfPage": {
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</label>
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<div class="gdoc-markdown--nested gdoc-tabs__content">
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<pre><code># 15 genomes
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demo.lmi: 69.89 MB
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56.65 MB seeds
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12.93 MB genomes
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312.53 KB masks.bin
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375.00 B genomes.map.bin
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323.00 B info.toml
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demo.lmi: 73.30 MB (73,297,328)
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59.41 MB seeds
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13.57 MB genomes
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320.03 kB masks.bin
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375 B genomes.map.bin
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323 B info.toml
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</code></pre>
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</label>
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<div class="gdoc-markdown--nested gdoc-tabs__content">
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<pre><code># 85,205 genomes
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gtdb_repr.lmi: 212.48 GB
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145.69 GB seeds
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66.78 GB genomes
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2.03 MB genomes.map.bin
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312.53 KB masks.bin
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gtdb_repr.lmi: 228.15 GB (228,149,871,198)
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156.44 GB seeds
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71.71 GB genomes
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2.13 MB genomes.map.bin
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320.03 kB masks.bin
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329 B info.toml
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</code></pre>
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</label>
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<div class="gdoc-markdown--nested gdoc-tabs__content">
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<pre><code># 402,538 genomes
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gtdb_complete.lmi: 906.04 GB
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543.06 GB seeds
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362.98 GB genomes
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9.60 MB genomes.map.bin
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312.53 KB masks.bin
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330.00 B info.toml
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gtdb_complete.lmi: 972.85 GB (972,854,821,322)
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583.10 GB seeds
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389.74 GB genomes
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10.06 MB genomes.map.bin
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320.03 kB masks.bin
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330 B info.toml
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</code></pre>
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</label>
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<div class="gdoc-markdown--nested gdoc-tabs__content">
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<pre><code># 2,340,672 genomes
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genbank_refseq.lmi: 4.94 TB
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2.77 TB seeds
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2.17 TB genomes
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55.81 MB genomes.map.bin
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312.53 KB masks.bin
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genbank_refseq.lmi: 5.43 TB (5,428,824,803,581)
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3.04 TB seeds
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2.38 TB genomes
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821.17 MB kmers-m12345.tsv
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58.52 MB genomes.map.bin
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320.03 kB masks.bin
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332 B info.toml
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</code></pre>
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</label>
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<div class="gdoc-markdown--nested gdoc-tabs__content">
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<pre><code># 1,858,610 genomes
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atb_hq.lmi: 3.88 TB
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2.11 TB seeds
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1.77 TB genomes
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39.22 MB genomes.map.bin
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312.53 KB masks.bin
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atb_hq.lmi: 4.26 TB (4,261,437,129,065)
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2.32 TB seeds
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1.94 TB genomes
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41.12 MB genomes.map.bin
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320.03 kB masks.bin
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332 B info.toml
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</code></pre>
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<li>Directory/file sizes are counted with <a
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class="gdoc-markdown__link"
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href="https://github.com/shenwei356/dirsize"
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>https://github.com/shenwei356/dirsize</a>. (base: 1024)</li>
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>https://github.com/shenwei356/dirsize</a> v1.2.1 (<code>dirsize -k</code>, base: 1000).</li>
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<li>Index building parameters: <code>-k 31 -m 40000</code>. Genome batch size: <code>-b 5000</code> for GTDB datasets, <code>-b 25000</code> for others.</li>
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</ul>
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<div class="flex align-center gdoc-page__anchorwrap">

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