Table 1

Major operations provided by the software package
Operations on entire DataSets: Opening and saving disk files in FASTA or FASTQ (Casava 1.8) format
Grooming disk files based on quality scores
Removing duplicate sequences
Removing non-coding sequences
Sorting sequence order by: pair end, sequence length, position of match to target sequence
Operations on selected sequences: Changing sequence length by addition or subtraction of bases
Shifting match position relative to a target sequence
Translation of sequence to amino acids
Moving sequences between DataSets
Editing sequence identity codes or descriptions
Operations for sequence discovery and assembly: Locating matching sequences in DataSets or disk files
Viewing sequence matches to a target sequence
Walking along a sequence by searching disk files
Finding missing paired ends and matching them to the target sequence
Melding matched sequences into a single sequence
Assembling sequences by simple overlap detection

All operations are initiated by bringing up a single menu (right click to screen) and selecting the operation.


French BMC Research Notes 2012 5:673   doi:10.1186/1756-0500-5-673

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