New manuscript and software package: SNIKT
Our team, led by Piyush Ranjan (lab bioinformaticist), has a new publication in Bioinformatics introducing SNIKT, a new software package we developed that automatically visualizes and removes adapter contamination from sequencing data. Adapters are short sequences added to nucleotide sequences to facilitate barcoding and sequencing. They are easily removed if you already know the adapter sequence, but this is often not the case with publicly available datasets. Our tool lets you quickly and effectively remove adapter contamination even if you don’t know the adapter sequence, and is platform-agnostic (works both on Illumina short reads and nanopore-derived long reads).
“SNIKT” stands for Slicing Nucleotides Into Klassifiable Tequences. “SNIKT” is the sound that Wolverine’s claws make when they emerge (we are Wolverines, after all). The “K” and “T” are loving winks to the error rate of nanopore sequencing.
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data
Piyush Ranjan