Tag: CD-HIT

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…

Continue Reading Petabase-scale sequence alignment catalyses viral discovery

Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

Continue Reading Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

Continue Reading Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

How to get a profile of consistent cd-hit clusters across different sequence files?

How to get a profile of consistent cd-hit clusters across different sequence files? 0 I have 10 different nucleotide sequence fasta files. I would like to run cd-hit on them and get a cluster abundance profile. If I run the fasta files on cd-hit separately, the clusters will not be…

Continue Reading How to get a profile of consistent cd-hit clusters across different sequence files?