polishing - aechchiki/SIB_LongReadsWorkshop_Zurich17 GitHub Wiki

The actual sequence of genome assembly is still not perfect, the calculation of consensus is limited by the quality scores of each base, however the signal is more complex than that.

Both PacBio and MinION have tools that exploit detailed information stored in raw sequencing data. The MinION consensus program is called Nanopolish and the consensus programs for PacBio are called quiver (for RSII) and arrow (for Sequel), delivered together in a package called GenomicConsensus.

Note that polishing is suited only for haploid sequences, here is a quote from GenomicConsensus FAQ :

"At present, quiver/arrow assume a haploid sample, and the behavior of on sample mixtures or diploid/polyploid samples is undefined."

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