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Nanopolish eventalign (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

Read alternative k-mer models (optional):

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

Only use reads with mapping quality of at least this value:

(-q)

Summarize the alignment of each read/strand:

Write the raw samples for the event to the tsv output:

Scale events to the model, rather than vice-versa:

write the raw signal start and end index values for the event to the tsv output:

write output in SAM format:

Print read names instead of indexes:

Usage: nanopolish eventalign [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa Align nanopore events to reference k-mers

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