LexicMap: efficient sequence alignment against millions of prokaryotic genomes

https://www.biorxiv.org/content/10.1101/2024.08.30.610459v1

'We introduce LexicMap, a nucleotide sequence alignment tool for efficiently querying moderate length sequences (> 500 bp) such as a gene, plasmid or long read against up to millions of prokaryotic genomes. '

Should be good for amplicons and #eDNA too???

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

Alignment against a database of genomes is a fundamental operation in bioinformatics, popularized by BLAST.

^bioRxiv

Long-distance Southern Ocean environmental DNA (eDNA) transect provides insights into spatial marine biota and invasion pathways for non-native species

https://www.sciencedirect.com/science/article/pii/S0048969724058133

#eDNA

A request to the #eDNA #environmentalDNA community. We are working on a project related to eDNA and ethics and looking for feedback from the user community. Please help us and complete this survey. https://forms.office.com/r/P6R57BAbZq Please pass it along to other users.

If you are a #conservation biologist, #ecology practitioner #molecularecology etc. or have been thinking of using the tool, we would like to hear from you.

Here's my poster for #ABACBS2023!

We compared different #eDNA taxonomic classifiers across different simulated datasets of 12S and 16S metabarcoding data.

MMSeqs2 generally 'wins' closely followed by BLAST.
With exclusion databases it becomes apparent that standard Kraken2 produces many, many false positives. With some families like snappers, all classifiers can't assign more than ~30% of sequences.

(not shown is COI, where MMSeqs2 and Mothur are working best)

Thanks @Helmholtz_HZI for the nice press release to accompany our study out now in @CurrentBiology: https://www.helmholtz-hzi.de/en/news-events/news/view/article/complete/dna-abstrich-von-blaettern-zeigt-enorme-vielfalt-der-regenwaldbewohner/

If you are a science communicator and have questions or are interested in covering our work - please get in touch! #SciComm #eDNA #PressRelease #NewPaper #Animals @Helmholtz_HIOH @unigreifswald

Detecting a vast diversity of rainforest animals by swabbing their DNA from leaves

Monitoring wildlife species present in specific areas is a critical first step to estimating the risk of transmission of infectious diseases to humans

^{Helmholtz Centre for Infection Research}