Baa.pl
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Application data |
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| Created by | Ryan JF |
|---|---|
| Biological application domain(s) | Sequence assembly (de novo assembly) |
| Principal bioinformatics method(s) | Sequence alignment analysis, Sequence assembly validation |
| Technology | Any |
| Created at | Sars International Centre for Marine Molecular Biology |
| Maintained? | Yes |
| Input format(s) | output from BLAT |
| Output format(s) | Plain text |
| Programming language(s) | Perl |
| Licence | GPL |
| Operating system(s) | any |
Summary: use transcripts to assess a de novo assembly
"Error: no local variable "counter" was set." is not a number.
Description
Simple script that parses the output of a BLAT run of a transcriptome vs. a genome assembly. It returns:
- Percentage of transcripts with a BLAT entry
- Total % coverage of all positions
- Number of transcripts mapping to a single contig/scaffold
- Average number of contigs/scaffolds mapped per mapped transcript
It also reports transcripts that show irregular alignments.
Useful for comparing genome assemblies, and reporting how well a particular assembly encapsulates the coding sequence of the genome.
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