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Rafał Wóycicki🚀 New bash pipeline for <a href="https://mastodon.social/tags/ddRADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#ddRADseq</a> preprocessing & deduplication! ✔️ Adapter trimming ✔️ Barcode demux ✔️ Cut site filtering ✔️ Pairwise dedup (w/ seqtk + awk) ✔️ Reproducible + lightweight📂 GitHub: <a href="https://github.com/rafalwoycicki/ddRADseq_reads" rel="nofollow noopener" translate="no" target="_blank">https://github.com/rafalwoycicki/ddRADseq_reads</a>🔁 RTs & feedback welcome! <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mastodon.social/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a>

Tyler SmithAt the end of a long day of <a href="https://ottawa.place/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> I've confirmed that I can cut my sequencing depth by half in the next round of sampling. Which means costs drop by half as well!By tomorrow we'll see if we can cut by another half again. Motivated by wanting to do <a href="https://ottawa.place/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a> / <a href="https://ottawa.place/tags/GBS" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBS</a> population <a href="https://ottawa.place/tags/genetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genetics</a> work on an octoploid plant. ugh!

Physalia-courses🚨Very happy to inform you that our <a href="https://ecoevo.social/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a> course is back!‼️🚀Save the date and join us in November to learn how to analyse your RADseq data with this stellar team of instructors <a href="https://mas.to/@naiara_re" class="u-url mention" rel="nofollow noopener" target="_blank">@naiara_re</a> @TerezaManousaki and @NataliaDA10 🤩✏️<a href="https://physalia-courses.org/courses-workshops/course16/" rel="nofollow noopener" translate="no" target="_blank">https://physalia-courses.org/courses-workshops/course16/</a> @RAD_seq

Physalia-courses🚨 Ready to master <a href="https://ecoevo.social/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a> data analysis with <a href="https://ecoevo.social/tags/Stacks" class="mention hashtag" rel="nofollow noopener" target="_blank">#Stacks</a>? Join our course led by the amazing @naiara_re, @TerezaManousaki, and @NataliaDA10!👉 Grab your spot here – only a few seats left! ⏳ <a href="https://www.physalia-courses.org/courses-workshops/course16/" rel="nofollow noopener" translate="no" target="_blank">https://www.physalia-courses.org/courses-workshops/course16/</a>

Julian CatchenWhat is the key element in a successful <a href="https://ecoevo.social/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a> experiment and analysis? How can you avoid the dreaded "missing data"?tldr; it's the quality of input DNA, and controlling the resulting levels of PCR duplicates that matters.Our latest work, led by Nicolas Rochette and Angel Rivera-Colón, (and in collaboration with Shane Campbell-Staton and Floragenex) shows this in great detail via modeling and experimental analysis. Now published in Molecular Ecology Resources: <a href="https://doi.org/10.1111/1755-0998.13800" rel="nofollow noopener" target="_blank">https://doi.org/10.1111/1755-0998.13800</a>

Physalia-courses🥁Registration is now open for the next edition of the <a href="https://mas.to/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a> <a href="https://mas.to/tags/dataanalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataanalysis</a> course with <a href="https://mas.to/@naiara_re" class="u-url mention" rel="nofollow noopener" target="_blank">@naiara_re</a> @TerezaManousaki & @NataliaDA10 Have a look at it: <a href="https://physalia-courses.org/courses-workshops/course16/" rel="nofollow noopener" target="_blank">https://physalia-courses.org/courses-workshops/course16/</a><a href="https://mas.to/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mas.to/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a>

Felix Zareie-VauxCool new study that quantifies sample cross-contamination, including laboratory mitigation methods: <a href="https://doi.org/10.1093/icesjms/fsad004" rel="nofollow noopener" target="_blank">https://doi.org/10.1093/icesjms/fsad004</a><a href="https://mastodon.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a> <a href="https://mastodon.social/tags/genetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genetics</a> <a href="https://mastodon.social/tags/GBS" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBS</a> <a href="https://mastodon.social/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a> <a href="https://mastodon.social/tags/fisheries" class="mention hashtag" rel="nofollow noopener" target="_blank">#fisheries</a> <a href="https://mastodon.social/tags/tuna" class="mention hashtag" rel="nofollow noopener" target="_blank">#tuna</a> <a href="https://mastodon.social/tags/fieldwork" class="mention hashtag" rel="nofollow noopener" target="_blank">#fieldwork</a> <a href="https://mastodon.social/tags/marinesci" class="mention hashtag" rel="nofollow noopener" target="_blank">#marinesci</a> <a href="https://mastodon.social/tags/marinebio" class="mention hashtag" rel="nofollow noopener" target="_blank">#marinebio</a> <a href="https://mastodon.social/tags/ecology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ecology</a> <a href="https://mastodon.social/tags/conservation" class="mention hashtag" rel="nofollow noopener" target="_blank">#conservation</a>

Felix Zareie-VauxTo get the ball rolling, I'd like to share a recent paper! Genotyping-by-sequencing for biogeography: <a href="https://doi.org/10.1111/jbi.14516" rel="nofollow noopener" target="_blank">https://doi.org/10.1111/jbi.14516</a>We provide a practical guide for <a href="https://mastodon.social/tags/biogeography" class="mention hashtag" rel="nofollow noopener" target="_blank">#biogeography</a> using <a href="https://mastodon.social/tags/GBS" class="mention hashtag" rel="nofollow noopener" target="_blank">#GBS</a> or <a href="https://mastodon.social/tags/RADseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RADseq</a>, which should particularly assist new users or students. There's a wealth of research exploring differences in reduced-representation sequencing (RRS) methods, sources of genotyping error, and much more. Our aim was to guide new users through this exciting literature. <a href="https://mastodon.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a> <a href="https://mastodon.social/tags/ecology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ecology</a> <a href="https://mastodon.social/tags/evolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#evolution</a> <a href="https://mastodon.social/tags/DNA" class="mention hashtag" rel="nofollow noopener" target="_blank">#DNA</a>

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