Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 5, Fall 6
Description
GOAL: To run NCBI's new tool for dealing with adapters and contaminants.
We run this on our TSA data and then resubmit.
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.
Attachments
Activity
Results of FCS-Adaptor found in /projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_adaptor
Going to investigate FCS-GX next
I think we should run this on a sequence run that we have changed the ID but with no additional filtering. This is so we can see how well it does, before and after, each step.
Brandon now adding slurm parallelization!
All runs finished. Successfully ran FCS-GX on cleaned files from FCS adaptor. Results are located in: /projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_GX/tom_runs/fin_results
Working on summarizing the results, but should be ready for another submission. Going to assign this to Dr. Reid for review
FCS tool results on tomato contigs: https://docs.google.com/spreadsheets/d/1fWZn0HTq1ZfM0hrL02CjD0nZ_5Q2frCkYH2945yOZDU/edit?usp=sharing
This looks great. However TSA still complains about the N's at the beginning and the end.
Which means we need to run your N filter after we do these filters!!!! Silliness.
This ticket is done, I'll create another.
Successfully ran FCS-adaptor on our Heinz contigs. I used the Heinz_new_ID_clean.fna as our input. I had to truncate the seqIDs even further because the tool splits the headers and adds a couple characters (ex: >lcl|H-contig-1-Solyc01T003576.3-1842). These extra characters exceed the 50 character limit, so it breaks the blast portion of this tool. Seqids went from >Heinz-contig-5-Solyc09T002714.1-2500 to >H-contig-5-Solyc09T002714.1-2500.
The final cleaned file is Heinz_cleaned_NCBI.fa and it is located in: /projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_adaptor/Heinz_NCBI
The fcs-adapt-commands.txt file lists all used commands and the order in which to use them. I will run this for other varieties as well.