GenotrickA pipeline for whole genome assembly and annotation of Genomes

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General

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Genotrick

• Data filter
• Genome assembly
• Genome annotation

Important Links

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

Sequencing data filtering

This module of Genotrick pipeline is designed to filter the raw sequencing data geneared by sequencers. Here, user can filter raw data of Illumina reads. 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) : Note:Please use paired-end reads or single-end reads at a time. Upload file containing single end reads:            Cut-off read length for High quality (%) e.g. 70 Cut-off Quality score (Interger)              e.g. 20 Primer/Adaptor libraries type          Genomic DNA/Chip-seq Library Paired End DNA Library DpnII gene expression Library NlaIII gene expression Library Small RNA Library Multiplexing DNA Library Do not filter for Primer/Adaptor FASTQ variants                              Sanger (Phred+33, 33 to 73) Solexa (Phred+64, 59 to 104) Illumina (1.3+) (Phred+64, 64 to 104) Illumina (1.5+) (Phred+64, 66 to 104) Illumina (1.8+) (Phred+33, 33 to 74) Automatic detection of FASTQ variant Email Address:

Example input files Following are example files of input raw short reads (i.e. paired end fastq reads) Forward reads (Mate-1) Reverse reads (Mate-2) Example output Files Following are the example output files, generated after running this server at default parameters (i.e. Cut-off read length for High quality was 70 and Cut-off Quality score was 20). Filtered forward reads (Mate-1) Filtered reverse reads (Mate-2) Filtered unpaired reads Report of data Filtering HTML Report of data Filtering

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