GenomeFLTR: Filtering reads made easy

Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothee Huchon*, Tal Pupko

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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:

Original languageEnglish
Pages (from-to)W232-W236
JournalNucleic Acids Research
Issue number1 W
StatePublished - 5 Jul 2023


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