AmpliTCR - Amplicon Sequencing T-Cell Receptor segments discovery tool

		
AmpliTCR analyzes a set of genomic or transcriptomic T-cell receptor (TCR) sequences by recognition and extraction of their Variable, Joining, Diversity, CDR3 and/or Constant regions, based solely on pre-defined protein patterns.


		AmpliTCR was designed to enable de novo identification of V, J and D segments from NGS targeted/amplicon sequencing reads that cover the entire Variable domain of the receptor (e.g. previously merged 300bp paired-end Illumina reads).

		Input DNA sequences are automatically translated into ORFs to extract TCR regions based on previously specified amino acid patterns.

		By default, sequences will be clustered with AmpliSAS-like algorithm optimized for Illumina technology and only unique TCR allele sequences segment specific will be retrieved (except for the CDR3 segment).

		

		

AmpliTCR workflow schema

		

		

		
AmpliTCR requires as input:

		
    
		
  • SEQUENCE FILE *: Reads from the experiment in a FASTQ or FASTA format file (compressed or uncompressed).
    • 
		
  • TCR REGION PATTERN/S: PROSITE format protein pattern/s to recognise TCR segments as explained in the documentation.
    • 
		

		      * This tool CANNOT use as input multiple sequence files packed into a unique .ZIP or .TAR.GZ file.

		

		

		Results can be downloaded on the same page or from an email message after analysis completion.


		Results will include a FASTA file containing all the TCR reads matching the desired TCR patterns and FASTA files containing the trimmed sequences of TCR segments according to the patterns.
		


		For more information, read the documentation.
		

		

	

		

		
Run AmpliTCR

		

		

		
Run name: 

		
Email (optional): 

		

		

			Sequence file:
			FASTA/FASTQ (compressed or uncompressed) without spaces, parenthesis or other special symbols in the name
 Max. 500 MB 
			Download example

					
		

		

		

			
			At least one segment pattern should be specified.
		

		

			Variable segment pattern: 
			
			
		

		

			Joining segment pattern: 
			
			
		

		

			Constant segment pattern: 
			
		

		

			
			PROSITE format syntax rules.
		

		

		

			
Additional options: 

		

		

			

		

		

			Number of reads to process: 
			
			Maximum number of sequences/reads to be processed.
		

		

			TCR constant segment primer: 
			
			Only sequences containing the primer will be processed.
		

		

			Cluster TCR segment sequencing errors with the following algorithm: 
			
			If selected this option, TCR segment trimmed sequences will be clustered to remove sequencing errors and discover alleles.

		

		

			Print protein sequences: 
			
			If selected this option, TCR segment translated sequences will be printed in additional FASTA files.

		


		



				
		
		
		

	

			
		
				

	
Disclaimer



		Your use of any of these tools is at your own risk.
		We do not give any representation or warranty nor assume any liability or responsibility for the data nor the results posted (whether as to their accuracy, completeness, quality or otherwise).
		Access to these data is available free of charge for ordinary use in the course of research.
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