Tools

In the last decade, advances in sequencing technology have led to an exponential increase in genomic data. These new data have dramatically changed our understanding of the evolution and function of genes and genomes. Despite improvements in sequencing technologies, identifying contaminated reads remains a complex task for many research groups. Here, we introduce GenomeFLTR, a new web server to filter contaminated reads. Reads are compared against existing sequence databases from various representative organisms to detect potential contaminants. The main features implemented in GenomeFLTR are: (i) automated updating of the relevant databases; (ii) fast comparison of each read against the database; (iii) the ability to create user-specified databases; (iv) a user-friendly interactive dashboard to investigate the origin and frequency of the contaminations; (v) the generation of a contamination-free file. Availability: https://genomefltr.tau.ac.il/.

GenomeFLTR: filtering reads made easy (2023)

Dotan E., Alburquerque M., Wygoda E., Huchon D., Pupko T.

Nucleic Acids Research website

Large-scale analyses of bacterial genomic datasets contribute to the comprehensive characterization of complex microbial dynamics among different strains and species. Such analyses require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome and error-prone due to manual handling. This motivated the development of the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting comparative microbial genomics analyses. Here we present M1CR0B1AL1Z3R-2.0. The pipeline input is a zipped folder with multiple FASTA-formatted files, each contains the genomic sequence of a single species/strain/isolate. The file can contain either a fully-assembled genome, a collection of contigs or the ORFs of a single genome. The main flow consists of extracting ORFs (if not provided as input), clustering them into groups of orthologs (orthogroups), inferring a core proteome, and reconstructing a phylogenetic tree.

M1CR0B1AL1Z3R 2.0 – A user-friendly web server for large-scale pan-genome analysis of microbial data (2019)

Shimony Y., Dotan E., Wygoda E., Wagner N., Ecker N., Lyubman I., Durante G., Mishan G., Chang J., Avram O., Pupko T.

website

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