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kmer-based clustering of transcript sequences

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tmer

Clusters transcripts by shared fixed-length kmers. This tool was originally devloped to detect redundant isoforms in transcriptome assemblies.

Usage example

To cluster transcripts use:

python tmer.py in_transcripts.fasta out_transcripts_clustered.fasta

Clustered transcript sequences in the output will be named according to >C[cluster_index]_[isoform_index].

Notes

This tool is intended to work with transcripts in the 10kb-100kb range.

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kmer-based clustering of transcript sequences

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