Tag: Megahit
Unexpected absence of ribosomal protein genes from metagenome-assembled genomes
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article PubMed Google Scholar Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS PubMed Article Google Scholar Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome
Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed PubMed Central Google Scholar Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…
Petabase-scale sequence alignment catalyses viral discovery
Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…
metagenome low alignment rate
metagenome low alignment rate 1 I have 20 metagenome samples which need to be analyzed. I started with one sample for the time being with the below tools/pipelines. After assembling first sample I mapped its reads back to contigs but the alignment rate is pretty low, What could be the…
many reads are not assembled into long contigs
many reads are not assembled into long contigs 2 Hi folks, I am assembling paired-end short metagnenomic reads (150 bp) using metaSpades and Megahit (with default settings). Then I did binning (with various binners and refiners), only 35-40% trimmed clean reads could be mapped to the bins. This is criticized…
Towards the biogeography of prokaryotic genes
1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed Google Scholar 2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS PubMed PubMed Central Google Scholar 3. Mohammad,…
