Script to assess the transcriptome assembly quality in terms of blastx and tblasn results?

Question

[seta]

Dear all,

As you better know, annotation matrix may be more suitable than length-based matrix for assessing transcriptome assembly quality. I read there is a single script that takes blastx and tblasn results of blasting your assembly against a database of interest and give you all information about the number of unique proteins found in the blastx search, the number of unique contigs hit by proteins in the tblastn search, the number of Reciprocal Best Hits, average Collapse Factor and average Ortholog Hit Ratio. Could anybody please put such a script here? your help would be really appreciated.

Answer 1

[rtliu]

Trinity: Full-length transcript analysis for model and non-model organisms using BLAST+

ANGUS 2.0: Scripts, Reciprocal Best-Hits BLAST

CRB-BLAST: Conditional Reciprocal Best Blast

[seta]

Thanks friend. I think there should be a script that cover all above-mentioned factor to assess transcriptome assembly quality, has anybody it?

[Farbod]

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Counting-Full-Length-Trinity-Transcripts