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1 This is the repository associated with the VAPPER Galaxy Tool available in the Galaxy Toolshed 1
2 VAPP accurately quantifies the variant antigen diversity in Trypanosoma congolense isolates or the variable Cog presence in T.vivax isolates 2
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5 The Trypanosoma congolense variant antigen repertoire is divided into 15 clades or phylotypes. These phylotypes are present in any T. congolense isolate, but their relative abundance varies between strains. The purpose of the VAPPER is to accurately quantify antigen diversity in any T. congolense isolate by calculating the relative frequency of each phylotype. 5
6 6
7 The Galaxy VAPPER Tool has three modes. 7 <!DOCTYPE html>
8 1) T.congolense Genomic: 8 <html lang="en">
9 This takes raw NGS reads (or pre-assmebled contigs) as input, assembles them de-novo, searches for evidence of each phylotype based on hidden Markov models (HMM), and calculates their relative abundances. 9 <head>
10 The results are visualized in three different ways: a table with each phylotype and their relative frequencies as proportions of the full repertoire in the given genome; a heat map with dendogram showing either absolute VAP variation or deviation from the mean, using our pilot dataset; and a Principal Component Analysis (PCA) plot showing variation distribution in the given sample compared to our pilot dataset. 10 <meta charset="utf-8">
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12 2) T.congolense Transcriptomic: 12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">
13 This requires NGS paired reads and uses bowtie2 and samtools for read mapping and processing, cufflinks for transcript abundance estimation, and hmmer for sequence identification. The output is a stacked bar chart and a table of frequencies based on the transcript abundances. 13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">
14 14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">
15 3) T.vivax clusters of orthologs 15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">
16 The approach for T. vivax relies on the presence/absence of clusters of orthologs (COGs). It requires velvet for the genome assembly and blast. it recieves paired sequencing reads in fastq format (or a contig file if already assembled) and the output is a binary matrix of the presence/absence of each COG/gene for a given sample. Within the tool there is a database of 28 isolates that are used as a comparison producing a heatmap and dendogram. 16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">
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716 <article class="markdown-body entry-content p-3 p-md-6" itemprop="text"><p>This is the repository associated with the VAPPER Galaxy Tool available in the Galaxy Toolshed
717 VAPP accurately quantifies the variant antigen diversity in Trypanosoma congolense isolates or the variable Cog presence in T.vivax isolates</p>
718 <p>The Trypanosoma congolense variant antigen repertoire is divided into 15 clades or phylotypes. These phylotypes are present in any T. congolense isolate, but their relative abundance varies between strains. The purpose of the VAPPER is to accurately quantify antigen diversity in any T. congolense isolate by calculating the relative frequency of each phylotype.</p>
719 <p>The Galaxy VAPPER Tool has four modes.</p>
720 <ol>
721 <li>
722 <p>T.congolense Genomic:
723 This takes raw NGS reads (or pre-assmebled contigs) as input, assembles them de-novo, searches for evidence of each phylotype based on hidden Markov models (HMM), and calculates their relative abundances.
724 The results are visualized in three different ways: a table with each phylotype and their relative frequencies as proportions of the full repertoire in the given genome; a heat map with dendogram showing either absolute VAP variation or deviation from the mean, using our pilot dataset; and a Principal Component Analysis (PCA) plot showing variation distribution in the given sample compared to our pilot dataset.</p>
725 </li>
726 <li>
727 <p>T.congolense Transcriptomic:
728 This requires NGS paired reads and uses bowtie2 and samtools for read mapping and processing, cufflinks for transcript abundance estimation, and hmmer for sequence identification. The output is a stacked bar chart and a table of frequencies based on the transcript abundances.</p>
729 </li>
730 <li>
731 <p>T.vivax clusters of orthologs
732 The approach for T. vivax relies on the presence/absence of clusters of orthologs (COGs). It requires velvet for the genome assembly and blast. it recieves paired sequencing reads in fastq format (or a contig file if already assembled) and the output is a binary matrix of the presence/absence of each COG/gene for a given sample. Within the tool there is a database of 28 isolates that are used as a comparison producing a heatmap and dendogram.</p>
733 </li>
734 <li>
735 <p>T.vivax Transcriptomic pathway
736 This method takes two NGS paired reads, maps the transcripts against a user supplied reference file and then estimates the trancript aboundance (using samtools and cufflinks). The output is then binned into 175 predefined phylotypes based on their greatest blastx similarity (this table is available in the results directory). A pident of less than 70% is considered unidentified. The results provide a tabular and graphical phylotype profile of the sample(s)</p>
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780 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
781 </a>
782 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
783 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li>
784 <li class="mr-3 mr-lg-0"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li>
785 <li class="mr-3 mr-lg-0"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
786 <li class="mr-3 mr-lg-0"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
787 <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
788 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
789
790 </ul>
791 </div>
792 <div class="d-flex flex-justify-center pb-6">
793 <span class="f6 text-gray-light"></span>
794 </div>
795 </div>
796
797
798
799 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
800 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
801 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
802 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
803 </button>
804 You can’t perform that action at this time.
805 </div>
806
807
808 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
809 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
810
811 <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script>
812
813
814
815 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
816 >
817 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
818 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
819 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
820 </div>
821 <template id="site-details-dialog">
822 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
823 <summary role="button" aria-label="Close dialog"></summary>
824 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
825 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
826 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
827 </button>
828 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
829 </details-dialog>
830 </details>
831 </template>
832
833 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
834 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
835 </div>
836 </div>
837
838 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
839
840 </body>
841 </html>
842