Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs

Background Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging...

biorxiv.org

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soeding_lab

soeding_lab @SoedingL

9 Aug 2024

Example: The number of full-length ssRNA phage genomes assembled from 82 metatranscriptomic samples from activated sludge and freshwater (Callanan, J. et al. Science Adv, 2020). PenguiN assembles ~3x more genomes (at 99% seqid filtering) than the next best assembler.

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soeding_lab

soeding_lab @SoedingL

9 Aug 2024

PenguiN, our viral metagenomics assembler, just got accepted at BMC Microbiome! In contrast to the standard de Bruijn graphs assemblers, it uses all-vs-all alignment in linear time to merge reads. This allows it to often resolve severalfold more strains than dBG assemblers.

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Patrick Cramer

soeding_lab retweeted

Patrick Cramer @mpgpresident

28 Apr 2020

Watching #coronavirus replication! #SARSCoV2 polymerase-RNA structure: basis to study potential #COVID19 drug #Remdesivir Team @hauke_hillen @KokicGoran @LucasFarnung @c_dienemann @DTegunov @mpi_bpc @maxplanckpress Preprint biorxiv.org/content/10.1101/… PR mpibpc.mpg.de/17275755/pr_20…

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