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jonas-fuchs/virHEAT: v.0.7
No full text<h2>Update virHEAT to 0.7</h2>
<h4>New</h4>
<ul>
<li>added <code>-s --scores</code> option that lets you link results from <a href="https://mavedb.org/">deep mutational screens</a> to the heatmap</li>
<li>added some more error catching</li>
<li>added MAVE example data</li>
<li>updated documentation</li>
</ul>
<p></p>
<h2>New Contributors</h2>
<ul>
<li>@PlushZ made their first contribution in https://github.com/jonas-fuchs/virHEAT/pull/13
Thanks a lot! :100:</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/jonas-fuchs/virHEAT/compare/v.0.6...v.0.7</p>
jonas-fuchs/varVAMP: v.1.2.0
No full text<h2><strong>Major varVAMP update to version 1.2</strong></h2>
<p>These changes are credited to @wm75 (https://github.com/jonas-fuchs/varVAMP/pull/39).</p>
<h3><strong>CHANGELOG</strong></h3>
<p><strong>(1) Changes around BLAST functionality:</strong></p>
<ul>
<li>Off-target amplicons are now reported as intended in the logs</li>
<li>Off-target amplicons are now always considered last for the final scheme (no penalty is used, but the fact that they had BLAST matches gets recorded)</li>
<li>The BLAST_PENALTY config option is no longer needed and has been removed</li>
<li>Added a new off_target_amplicons column to the qPCR design, the qPCR primer and the (single/tiled) primer tsv outputs to indicate which final amplicons had BLAST hits</li>
</ul>
<p><strong>(2) General reporting changes:</strong></p>
<ul>
<li>Amplicon numbering now proceeds from 5' to 3' even across pools for the tiled mode and from lowest penalty to highest for the other modes (previously additional BLAST penalties weren't considered during penalty-sorting).</li>
<li>In the primer bed file output in tiled mode, primers are now ordered according to the amplicon number without taking the pool into account</li>
<li>In the primer bed file output in qPCR mode, oligos from the same set are now ordered LEFT, PROBE, RIGHT, i.e. by position on the reference</li>
<li>The per-base mismatch plot now uses final primer names as panel titles</li>
<li>The amplicon bed file, in all modes, is now formatted as proper six-column bed</li>
</ul>
<p><strong>(3) Algorithmic fixes and enhancements:</strong></p>
<ul>
<li>The internal representation of amplicon schemes has been unified/simplified across the different modes and steps of the analysis</li>
<li>Search for final non-overlapping amplicons in single mode and for non-overlapping amplicons passing deltaG in qpcr mode has been optimized and is now significantly faster</li>
<li>Some off-by-one errors in internal primer and amplicon interval calculations have been fixed - generally more primers are now found and considered</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/jonas-fuchs/varVAMP/compare/v.1.1.3...v.1.2.0</p>
jonas-fuchs/virHEAT: v.0.6
No full text<p><strong>NEW</strong></p>
<ul>
<li>added <code>--zoom</code> option that allows to zoom into genomic region specified by <code>start</code> and <code>stop</code> values.</li>
<li>added <code>--name</code> option that allows to customize the name of the plot and the file type. If none is given the default is still <code>virHEAT_plot.pdf</code></li>
</ul>
<p><strong>FIXES</strong></p>
<ul>
<li>Error catching if the gff3 is missing a region annotation (needed to get the correct genome length)</li>
<li>small code structural changes</li>
</ul>
jonas-fuchs/virHEAT: v.0.5.4
No full text<p>NEW:</p>
<ul>
<li>added the <code>-n</code> option that allows to delete mutations that appear in the heatmap n times or less. Will be applied after all filtering steps.</li>
</ul>
<p><em>Example: <code>-n 1</code> will delete all mutations indepent of their frequency if they appear only once in the heatmap. Particular helpful to declutter the heatmap and focus on specific mutations that e.g. appear and increase in frequency over time.</em></p>
jonas-fuchs/BAMdash: v.0.2
No full text<p><strong>NEW</strong></p>
<ul>
<li>full SNP and INDEL annotation if they lie in a CDS</li>
<li>bin size for coverage plot</li>
</ul>
jonas-fuchs/ViralPrimerSchemes: v.0.1
No full text<p>First release that includes evaluated and non-evaluated primer schemes for tiled sequencing and qPCR of various highly variable virus. Primers were exclusively designed with varVAMP!</p>
jonas-fuchs/varVAMP: v.0.8
No full textNEW:
integrated automatic parameter selection for -t, -a and -pa
FIXES:
Fixed small plotting issue.
Fixed a bug if -a was set to 0
changed "conserved regions" to "primer regions" as this could be misleading.
updated documentation accordingl
jonas-fuchs/varVAMP: v.0.8.1
No full textHOTFIX
Fixed:
Bug that at certain settings the alignment cleaning could produce an empty list, leading to a crash
Bug with the automatic parameter selection where the last frequency was not appended, leading to a high underestimation of the parameters if the alignment had no positions that fell under the frequency threshold cutoff that starts at 0.1
changed a small typo in the log file
updated versio
jonas-fuchs/varVAMP: v.1.0
No full text<p><strong>NEW</strong></p>
<ul>
<li>added fasta output for primers</li>
<li>new workflow.png in the "How varVAMP works" section</li>
<li>renamed <code>n_threads </code> argument to <code>threads</code></li>
</ul>
<p><strong>FIXES</strong></p>
<ul>
<li>renamed scores to penalties at several pos in the code to avoid confusion.</li>
<li>code reformatting and clearer documentation</li>
<li>more intuitive way of how polyX and polyXY are counted (prior three repeat was equal to the Primer setting <code>MAX_POLYX </code> = 3, but meant that stretches of e.g. 4 As were tolerated). Now the counting was adjusted so that <code>MAX_POLYX </code> = 4 is equal to the prior <code>MAX_POLYX </code> = 3.</li>
<li>renamed primer names in a more intuitive manner. The old primer names are now given as alternate names in the tsv.</li>
</ul>
jonas-fuchs/varVAMP: v.1.0.1
No full text<p><strong>NEW</strong>
changed SANGER mode to SINGLE mode. Better naming to what this modus actually does. Design primers for single amplicons.</p>
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