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Trycycler subsample (version 0.5.5)
--reads
The number of subsamples reads to make maximally-independent read subsets. The default is 12, a good number for most cases.
If you do not provide this, Trycycler subsample will run miniasm to quickly assemble your read set to get a size. This value is used to calculate read depths and does not need to be exact, e.g. 10% error is fine.
An estimate of the isolate total genome size.
This is the minimum allowed read depth and also controls the subsampled depths. If is not provided, Trycycle decides what read depth each subset will be.

Purpose

The Trycycler subsample tool tries to make maximally-independent read subsets of an appropriate depth for your genome. The goal is to use each subsample for generating varios assemblies by using different assemblers. It will also be handy to know the approximate size of your genome. If you're assembling something novel (i.e. you don't know the genome size), you could do a quick initial assembly at this point to get an estimate.


Input

This tool requires a long-read dataset. Ideally your reads should have a coverage of at least 100x.


Output

The result is a number of subsampled read sets, whose number is determined by the count parameter.


Trycycler pipeline

Trycycler subsample: make maximally-independent read subsets of an appropriate depth.
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Trycycler cluster: carries out complete-linkage clustering of all contig sequences.
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Trycycler reconcile/msa: reconcile the contigs within each cluster and perform a multiple sequence alignment.
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Trycycler partition: split the reads between the different clusters.
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Trycycler consensus: generate a consensus contig sequence for each cluster.