SqueezeMeta is our metagenomic/metatranscriptomic pipeline, filling all the steps of the analysis from assembly to gene prediction, taxonomic and functional annotations, and binning. SqueezeMeta supports multi-metagenomic analysis, in which several samples can be simultaneously analyzed. SqueezeMeta is a widely used tool, used in the analysis of more than 80 published metagenomes.
Download it from github
or read the Frontiers paper here
SqueezeMeta also includes SQMtools,a R library for easy inspection and manipulation of the results. See the paper here
Coming soon, ShinySQM will allow interactive graphical display of the results, making it possible to share results with remote users.
microDB is a database that aims to provide the most complete census to-date of the environmental distribution of prokaryotes. microDB connects the taxonomic identification of 16S rDNA sequences with the environmental characterization of their original samples. This is the result of a comprehensive effort to annotate all samplings and sequences stored in the ENV section of GenBank database. Currently, microDB contains 2934014 sequences belonging to 21104 samples
Cover is an interactive web tool for aiding in the precise design of the experiment, and to guide the researcher on the proper amount of DNA sequencing needed. Cover allows the prediction of the results obtained with a particular amount of sequencing, in terms of the coverage achieved for each of the species in the sample. Cover is capable to correct for the number of unobserved species in the simple
|Bacteria in hot springs, from Costa Rica to Antarctica (English)
|Art i ciència: Picasso i l’estructura del DNA (Català)
Aula Blanes 4 June 2013
|Bacteria and climate change (English)
CREAF, 22 November 2017