Features

FastQ encoding auto detection

• SFF
• FastQ, FQ
  • Auto-detect encoding
  • Sanger encoding
  • Solexa encoding
  • Illumina 1.0, Illumina 1.3, Illumina 1.5, Illumina 1.8 encoding
• FastQ encoding auto detection

Filters

• Cut poly-A/T tails
• Cut reads with average QV under specified threshold
• Cut reads if they contain N bases (the user can specify how many)
• Cut low complexity reads
• Cut reads that are too short
• Cut reads that are too long
• Cut low quality ends. Automatically detect and cut low quality bases at the end of each read

Tools and converters

• Split multiplexed files (MID/Barcode splitter)
• Remove contaminants (search over represented sequences against a contaminant database)
• Dereplicate sequences (under development)
• File splitter: Split huge FastQ/SFF file in chunks of x reads
• File splitter: Cut all sequences in the specified range
• Compact FastQ files
• Convert SFF to FastQ
• Convert SFF to Fasta
• Convert FastQ to Fasta (multiFasta)
• Convert FastQ file to a different encoding (under development)

Graphs and data analysis

• Read lister - Show read name, base sequence, average quality, sequence length
• Graphic quality representation for each individual read. Color coded.
• Sequence length distribution graph
• Per base sequence quality graph
• Per base GC content graph
• Per base sequence content graph
• Per base N content graph (integrated in the 'Per Base Content' graph)
• Per sequence quality scores graph graph
• Duplication level graph
• Overrepresented sequences table

• Graphs can be expanded to full screen
• All graphs are updated in real time as the file is processed!
• File statistics: file name, file size, number of reads (before and after filtering), encoding, per file GC percent
• The analysis of the current file (including all graphs) can be saved as HTML report

GUI / System

• Easy to use/configurable GUI
• Save/remember GUI state
• Open SFF/FastQ files when user double clicks them in Windows Explorer
• Open file passed via command line
• Easy to use file browser (allows you to quickly locate your FastQ/SFF files)
• Long operations can be easily canceled

Related tools:

• NCBI BLAST DB Downloader is a a freeware biology software tool that automates the NCBI BLAST DB download process.
• NCBI Blaster (aka BLAST Robot) is a software tool that automates the NCBI BLAST search processes.