SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data

SUMMARY: Here, we introduce SNIKT, a command-line tool for sequence-independent visual confirmation and input-assisted removal of adapter contamination in whole-genome shotgun or metagenomic shotgun long-read sequencing DNA or RNA data. AVAILABILITY AND IMPLEMENTATION: SNIKT is implemented in R and is compatible with Unix-like platforms. The source code, along with documentation, is freely available under an MIT license at https://github.com/piyuranjan/SNIKT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.