Αποθηκεύτηκε σε:
| Κύριος συγγραφέας: | |
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| Μορφή: | Recurso digital |
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Zenodo
2025
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| Διαθέσιμο Online: | https://doi.org/10.5281/zenodo.18196708 |
| Ετικέτες: |
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Πίνακας περιεχομένων:
- <h2>What's Changed</h2> <ul> <li>Integration of VAMB in the pipeline by @baptwr in https://github.com/UMMISCO/strainmake/pull/1</li> <li>Integration of Binette in the pipeline by @baptwr in https://github.com/UMMISCO/strainmake/pull/2</li> <li>Integration of GTDB-Tk in the pipeline by @baptwr in https://github.com/UMMISCO/strainmake/pull/3</li> <li>Handling several samples at once by @baptwr in https://github.com/UMMISCO/strainmake/pull/5</li> <li>Integration of dRep in the pipeline and changes in Binette by @baptwr in https://github.com/UMMISCO/strainmake/pull/6</li> <li>Integration of MetaPhlAn 4 in the pipeline by @baptwr in https://github.com/UMMISCO/strainmake/pull/7</li> <li>Using long reads and short reads by @baptwr in https://github.com/UMMISCO/strainmake/pull/8</li> <li>Using VAMB v4 and using VAMB with GPUs by @baptwr in https://github.com/UMMISCO/strainmake/pull/9</li> <li>Using SPADes for hybrid assembly by @baptwr in https://github.com/UMMISCO/strainmake/pull/10</li> <li>Integration of Floria and inStrain to profile samples (SR only) by @baptwr in https://github.com/UMMISCO/strainmake/pull/11</li> <li>Script for using Skani comparison on produced bins by @baptwr in https://github.com/UMMISCO/strainmake/pull/12</li> <li>Script for calculating the binned contigs rate by @baptwr in https://github.com/UMMISCO/strainmake/pull/13</li> <li>Adding basic tests by @baptwr in https://github.com/UMMISCO/strainmake/pull/17</li> <li>Filtering out short contigs based on configuration by @baptwr in https://github.com/UMMISCO/strainmake/pull/18</li> <li>Reducing storage footprint by @baptwr in https://github.com/UMMISCO/strainmake/pull/22</li> <li>Measuring the runtime of each job by @baptwr in https://github.com/UMMISCO/strainmake/pull/23</li> <li>GTDB-Tk annotation of dereplicated and filtered bins by @baptwr in https://github.com/UMMISCO/strainmake/pull/24</li> <li>inStrain for long reads by @baptwr in https://github.com/UMMISCO/strainmake/pull/27</li> <li>Supporting long reads in FASTA format by @baptwr in https://github.com/UMMISCO/strainmake/pull/30</li> <li>Refactoring, downsizing samples for hybrid approaches by @baptwr in https://github.com/UMMISCO/strainmake/pull/31</li> <li>Building gene catalogs from assemblies by @baptwr in https://github.com/UMMISCO/strainmake/pull/33</li> <li>Integration of Meteor for taxonomic profiling by @baptwr in https://github.com/UMMISCO/strainmake/pull/34</li> <li>Integration of CarveMe for metabolic modeling by @baptwr in https://github.com/UMMISCO/strainmake/pull/35</li> <li>Using MMseqs2 instead of CD-HIT by @baptwr in https://github.com/UMMISCO/strainmake/pull/36</li> <li>Adding HyLight for hybrid assembly by @baptwr in https://github.com/UMMISCO/strainmake/pull/37</li> <li>Helping to generate configuration/Snakefile by @baptwr in https://github.com/UMMISCO/strainmake/pull/39</li> <li>Using fastplong by @baptwr in https://github.com/UMMISCO/strainmake/pull/41</li> <li>Integration of Bakta for MAG annotation by @baptwr in https://github.com/UMMISCO/strainmake/pull/42</li> <li>Adding unit tests by @baptwr in https://github.com/UMMISCO/strainmake/pull/43</li> <li>A Docker image for the pipeline by @baptwr in https://github.com/UMMISCO/strainmake/pull/45</li> <li>Using CHM13 v2 instead of GRCh38 by @baptwr in https://github.com/UMMISCO/strainmake/pull/47</li> <li>Specifying minor/patch versions of various tools by @baptwr in https://github.com/UMMISCO/strainmake/pull/48</li> <li>A CLI for MultiQC report by @baptwr in https://github.com/UMMISCO/strainmake/pull/50</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/UMMISCO/strainmake/commits/v0.1.0-pre1</p>