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Nanopolish variants (version 0.14.0+galaxy0)

Basecalled merged reads.fa:

Flat archive file of raw fast5 files:

Reads aligned to the reference genome:

Load reference genome from:

Using reference genome:

REFERENCE_SEQUENCE

Optional data inputs

Optional data inputs 0

find variants in window of region chromsome:start-end:

methylation aware polishing and test motifs given:

(-q)

Extarct if the variant frequency is at least F:

(-m)

Extarct if the depth is at least D:

(-d)

Consider at most N haplotype combinations:

(-x)

Perform N rounds of consensus sequence improvement:

(--max_rounds)

The ploidy level of the sequenced genome. -1:disabled:

(-p)

Distance from alignment end to calculate variants:

(--min-flanking-sequence)

Consensus calling mode and output polished sequence:

only call SNPs:

verbose output:

homopolymer caller:

speedup while slightly reducing consensus accuracy:

calculate the support of the 3 other possible bases:

Build an index mapping from basecalled reads to the signals measured by the sequencer and find SNPs using a signal-level HMM.

Tutorial and manual available at: http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html