Which steps are executed when performing a de novo assembly on the calculation engine?

Question: 

Which steps are executed when performing a de novo assembly on the calculation engine?

Answer: 

Assembly using SPAdes

First, an automated trimming is performed on the reads (see KB article) followed by the SPAdes[1] de novo assembly with read error correction (BayesHammer (Illumina) or IonHammer (IonTorrent)). BWA-MEM[2] is used to map the reads back to the SPAdes assembly followed by a consensus calling based on the mapping, serving as an additional mismatch correction.

Assembly using Velvet

First, an automated trimming is performed on the reads (see KB article) followed by the actual Velvet[3] de novo assembly on the trimmed reads. Bowtie2[4] is used to map the reads back to the Velvet assembly followed by a consensus calling based on the mapping, serving as an additional mismatch correction.

 

[1] Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski, et al. Spades: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5):455–477, 2012.

[2] Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.

[3] D.R. Zerbino and E. Birney. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome research, 18(5):821, 2008.

[4] Ben Langmead and Steven L Salzberg. Fast gapped-read alignment with bowtie 2. Nature methods, 9(4):357–359, 2012.

 

 

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