GenotrickA pipeline for whole genome assembly and annotation of Genomes

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Genotrick

• Data filter
• Genome assembly
• Genome annotation

Important Links

• NGS QC toolkit
• Velvet
• PROKKA
• Genomics web Portal
• GenomeABC

Short Reads assembly

This module of Genotrick pipeline is designed to assemble whole genome of an organism from short reads (Illumina type). Whole genome assembly is performed with the help of Velvet software, at user defined parameters.For more information, please click HERE To demostrate the server, please use the example input files.

Illumina data submission Paired end short sequencing reads (i.e. Illumina reads) can be uploaded here. Please upload both files having forward and reverse reads, for detail (e.g. format) see example files in right column. Upload file containing forward reads (Mate-1) : Upload file containing reverse reads (Mate-2) : Upload file containing single end reads:            Genome assembler parameteres Hash length (K) for genome assembly       e.g. 21 Covearge of Genome Sequencing              e.g. 60 Insert length                                                e.g. 350 File format option                          fasta fastq fasta.gz fastq.gz Read type option                          short shortPaired long longPaired Scaffolding                                    Yes No Email Address:

Example input files Following are example files of input short reads (i.e. paired end fastq reads) Forward reads (Mate-1) Reverse reads (Mate-2) Example output Files This is the contigs file generated after the assembly of input reads (i.e. paired end fastq reads) by this server at hash length 71 and coverage 60.Contigs generated

Note: Large amount of data processsing may be difficult at this server. User are advised to use standalone version for large data.