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SSAKE (version 0.0.10)

Kind of reads (-p):

Input FASTA file:

FASTA file containing sequences to use as seeds exclusively (-s):

Optional, specify only if different from read set

Minimum depth of coverage allowed for contigs (-w):

Minimum number of overlapping bases with the seed/contig during overhang consensus build up (-m):

Minimum number of reads needed to call a base during an extension (-o):

Minimum base ratio used to accept a overhang consensus base (-r):

What it does

SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences. It is an easy-to-use, robust, reliable and tractable clustering algorithm for very short sequence reads, such as those generated by Illumina Ltd.

License and citation

If you use this tool in Galaxy, please cite Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics, accepted.

This tool uses SSAKE, which is licensed separately. Please cite Warren RL, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23(4):500-501.