Version 2.5.0 of SPAdes single-cell assembler has been just released.
The main feature of the new version is the support for multiple paired-end and mate-pair libraries. By using the command line interface you can specify up to 5 libraries of each type and, as previously, unlimited number of single read libraries. However, you can write to our support if you need to assemble more libraries simultaneously.
Also, we changed repeat resolution strategy and thus decreased mismatch and indel rates comparing to the previous versions.
You can download SPAdes 2.5 here.
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