GOAL: To run NCBI's new tool for dealing with adapters and contaminants.
We run this on our TSA data and then resubmit.

https://github.com/ncbi/fcs

FCS
The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.

FCS-adaptor
FCS-adaptor detects adaptor and vector contamination in genome sequences. FCS-adaptor is a high-throughput implementation of NCBI VecScreen. The FCS-adaptor executable retrieves a Docker or Singularity container and runs a pipeline to screen input sequences against a database of adaptors and vectors using stringent BLAST searches.

Please read the wiki for instructions on how to run FCS-adaptor.

FCS-GX
FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). The FCS-GX executable retrieves a Docker or Singularity container and runs a pipeline to align sequences to a large database of NCBI genomes through modified k-mer seeds and assign a most likely taxonomic division. FCS-GX classifies sequences as contaminant when their taxonomic assignment is different from the user-provided taxonomic identifier.

Please read the wiki for instructions on how to run FCS-GX.