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Editor to share with you what are the advantages and disadvantages of the CD-HIT merger strategy in Pacbio, I believe most people do not know much about it, so share this article for your reference, I hope you can learn a lot after reading this article, let's go to know it!

Transcript merging Strategy of the third Generation non-reference full-length Transcriptional Group (IsoSeq3) in Pacbio

The third-generation full-length transcriptome of Pacbio uses IsoSeq3 to filter, merge and correct transcripts to get high-quality transcripts, but there is still some sequence redundancy between these transcripts, which requires a certain sequence merging operation.

Pacbio officials currently recommend two strategies: using CD-HIT merging and using Cogent for gene prediction and sequence merging.

Now compare the advantages and disadvantages of the two strategies:

Pros and cons of the CD-HIT merger strategy:

1. Advantages:

1.1 the merging speed is fast, and cd-hit is a classic software, which is often used in transcriptome analysis.

1.2 the results are easy to understand: the software simply merges transcripts based on sequence similarity, and the ID of transcripts will not change.

two。 Disadvantages:

2.1 it is impossible to distinguish which transcripts come from the same gene.

2.2 unable to provide transcript sequence quality information

Cogent merger strategy

1 advantages:

1.1 provides information on gene and transcript levels, and of course this so-called gene level is only an analytical strategy for Cogent

1.2 also supports certain sequence quality screening, such as coverage.

2 shortcomings

2.1 the software takes a long time to run and its speed is relatively slow. And the installation of Cogent software is troublesome.

2.2 the results are not easy to understand: Cogent will first cluster the sequences, and then merge the sequences to get longer gene region sequences.

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