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tseemann / shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
GNU General Public License v3.0
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Assembly statistics #96

Open marchoeppner opened 6 years ago

marchoeppner commented 6 years ago

Hi,

thanks for this tool, already incorporated it into one of our pipelines. That said, I think it currently does not output an assembly statistic file, like Spades does? This would be useful especially in a higher throughput setting for downstream QC. Any chance this could be added (ideally identical to the spades statistics so that it could be integrated with MultiQC).

Cheers, Marc

darwinbandoy commented 6 years ago

I also have the same request- output statistics like N50, contig length etc would be useful. I think I can see it in the log file but log file is too verbose for a quick scan. Another feature request is a summary statistics for a batch file- as we usually do this manually for each assembly and compile it in an excel file. Similar to the summary feature of abricate- a summary feature for shovill in batch assembly can be a time saver.

tseemann commented 5 years ago

@marchoeppner I think an assembly stats output in a machine readable form is a good idea.

@darwinbandoy I won't be adding an "aggregate report" option though; that is best done by a dedicated tool like MultiQC (or Nullarbor)