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SSPACE for Debian
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Please note: This is the free 'basic' version of SSPACE. The non-free
'standard' version is available directly from Baseclear at
http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
SSPACE tracks in memory all contigs. That means that the memory usage
will increase drastically with the size of your contig data set. In
addition, during contig extension single reads are extracted and mapped
to the contigs. Unmapped reads are stored in memory. Again, the more
reads that can not map, the bigger the dataset and the more memory is
used. Just be aware of these limitations and don't be surprised if you
observe a lot of data swapping to disk if you attempt to run SSPACE on a
machine with little RAM.
Contig extension might not be suited to work with 454-type read pair
libraries. Simply because recurring base insertions/deletions errors,
such as those commonly seen in homopolymeric regions, will not cluster
well in the context of the SSAKE contig extension algorithm scheme. In
addition, long 454 reads are less likely to map against the contigs,
thus less read pairs are found and scaffolding is based on less read
pairs. One possibility is to allow gaps during mapping using the æ-gÆ
parameter.
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