SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau.ru/en/spades.
Manual at http://spades.bioinf.spbau.ru/release3.7.1/manual.html
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Common usage
SPAdes: de Bruijn graph based assembler
The last assembler we will run is SPAdes. SPAdes is different from the other assemblers in that it generates a final assembly from multiple kmers. A list of kmers is automatically selected by SPAdes using the maximum read length of the input data, and each individual kmer contributes to the final assembly. To run SPAdes we will use the
spades.pycommand with the--carefuloption to minimize the number of mismatches in the contigs,-ofor the output folder,-1for the path to the forward reads,-2for the path to the reverse reads, and-sfor the path to the singles reads. If desired, a list of kmers can be specified with the-kflag which will override automatic kmer selection.