Additional file 1 of Wochenende — modular and flexible alignment-based shotgun metagenome analysis
Creators: name: Rosenboom, Ilona
name: Scheithauer, Tobias
name: Friedrich, Fabian C.
name: Pörtner, Sophia
name: Hollstein, Lisa
name: Pust, Marie-Madlen
name: Sifakis, Konstantinos
name: Wehrbein, Tom
name: Rosenhahn, Bodo
name: Wiehlmann, Lutz
name: Chhatwal, Patrick
name: Tümmler, Burkhard
name: Davenport, Colin F.
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Additional file 1: Supplementary Figure S1. Genome coverage plot of B.intestinalis reported by Wochenende. Wochenende did not misclassify B. subtilis in the mock community by Sui et al (SRSRR11207337) [29], but rather detected B. intestinalis with a high and evenly distributed coverage. Indeed all the other tools also reported B. intestinalis instead of B. subtilis. Supplementary Figure S2. Wochenende analysis of an alternative long-read Zymo Even DNA mock community. The mock community was sequenced on an Oxford Nanopore GridION sequencer by the laboratory of Nick Loman (https://github.com/LomanLab/mockcommunity). To our knowledge, the other tested tools are not able to analyze these long reads appropriately. The dataset and analysis is plausible yet suboptimal, as none of the species was found within their expected range, though Enterococcus faecalis, Staphylococcus aureus and Listeria monocytogenes come close. Lactobacillus fermentum is present at higher abundance than the expected range. B.subtilis is again underrepresented, similarly to the results from short read data presented in Figure 2 [29]. Supplementary Figure S3. A heat tree automatically produced by our tool Haybaler using the R package metacoder. The taxonomy of this fairly typical airway metagenome is illustrated succinctly and is useful for rapid initial comparative analyses across samples. Rothia mucilaginosa and Haemophilus influenzae dominate, though diverse Streptococcus and several Veillonella and Prevotella species are also present. Supplementary Figure S4. Reads from a skin swab were mapped to a fungus from the Wochenende reference genome. These reads were mapped with high mapping quality to all Candida tropicalis supercontigs, providing a rare example of a fungus in this metagenome. Fungi are generally difficult to reliably locate in metagenomes because of low abundance, poor reference genomes and wet lab sampling bias due to their highly resistant physical structures. Fungi remain rare in our experience of hundreds of particularly airway metagenomes, despite frequent reanalysis. It is not unexpected to find C. tropicalis at higher biomass in a skin sample, as opposed to our usual lung samples, but demonstrates our pipeline’s utility in locating eukaryotes. Supplementary Table S1. Results from Kaiju on the same mock community dataset SRR11207337 analyzed in Figure 2. Eight bacteria should be present at 12%, with two fungi at 2% each. Results were only at genus level and are therefore reported here.