Purpose

The Trycycler partition split the reads between the different clusters, i.e. each read will be assigned to whichever cluster it best aligns and saved into a file for that cluster. This step is run once for your entire genome (i.e. not on a per-cluster basis).

Input

This tool requires as input the set of clustered considered valuable, and the long-read dataset used previously.

Output

After Trycycler partition completes, if will generate a file per cluster, each of which contains its share of the total reads.

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.