AmpliMERGE - Amplicon Sequencing MERGing tool

		
AmpliMERGE merges paired-end reads from next-generation sequencing experiments.


		Some NGS technologies can read amplicon sequences from both sides (covering partially or totally the
		amplified region) and retrieve paired-end reads that overlap (e.g. Illumina Mi-Seq). These paired-end reads must
		be merged into a unique sequence before continuing the data analysis. The merging process will correct errors in
		low quality sequenced positions and will increase the length of the sequence if it was not fully covered by any
		of the paired-end reads.



		AmpliMERGE runs in background the FLASH algorithm with optimum overlapping parameters:

		

		

		
AmpliMERGE takes as input:
		
    
		
  • SEQUENCE FILE R1: First paired-end reads file in FASTQ or FASTA format (compressed or uncompressed). Multiple files should be named '*_R1.*' and packed into a unique .ZIP or .TAR.GZ file.
    • 
		
  • SEQUENCE FILE R2: First paired-end reads file in FASTQ or FASTA format (compressed or uncompressed). Multiple files should be named '*_R2.*' and packed into a unique .ZIP or .TAR.GZ file.
    • 
		
  • AMPLICON DATA *: primer and tag information in a CSV format file as explained in the documentation.
    • 
		

		      * This file is not required if the 'Sequence File' already contains multiple files packed together.
		

		

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


		Output files will be in FASTQ compressed format, ready to be used in other AmpliSAT tools like AmpliCHECK or AmpliSAS.
		


		For more information, read the documentation.
		

	

		

		
Run AmpliMERGE

		

		

		
Run name: 

		
Email (optional): 

		

			

		

		

			Paired-end reads file R1:
			FASTQ (compressed or uncompressed)
 Max. 500 MB 
			Download example

			
			


			If reads have been already de-multiplexed into separate files (one file per sample), 
			you can pack them into a single .zip or .tar.gz format file and use it as input.
			In such case file 1 and file 2 must have identical names and differ only in the suffixes '_R1' and '_R2'.

					
		

		

			

		

		

			Paired-end reads file R2:
			FASTQ (compressed or uncompressed)
 Max. 500 MB 
			Download example

			
					
		

		

			

		


		

		

		
		

			
			Advanced program parameters


			
		

		


				
		
		
		


	

			
		
				

	
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