Galaxy | Tool Preview

Trycycler partition (version 0.5.5)
Clustered contigs (multiple FASTA files)
Long reads (FASTQ format) used to generate the assemblies
Reads with less than this many bases aligned (default = 1000) will be ignored.
Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.


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).


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


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