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PATRIC3 / patric3_website

Legacy PATRIC Website (JBoss Portal Version)
MIT License
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Assembly Service enhancements #517

Closed rkenyon closed 8 years ago

rkenyon commented 9 years ago

In this release, we will enable assembly of genomes sequenced using PacBio technology. Both raw m5 read files and filtered FASTQ files from PacBio sequencing will be accepted as input.

rkenyon commented 9 years ago

10/14 update: On target for November, per Fangfang

rkenyon commented 9 years ago

10/28: Ron check with Fangfang.

rkenyon commented 8 years ago

11/18: Ron check with Fangfang. Minor UI changes to add PacBio to list

levinas commented 8 years ago

I've redeployed the assembly service with experimental pacbio/nanopore support. @aswarren Can you please update the help text for the Parameters section?

auto

For short reads:

  1. Runs BayesHammer on reads
  2. Assembles with Velvet, IDBA and SPAdes
  3. Sorts assemblies by ALE score

For long reads (PacBio or Nanopore): Assembles with MiniASM

smart

For short reads:

  1. Runs BayesHammer on reads, Kmergenie to choose hash-length for Velvet
  2. Assembles with Velvet, IDBA and SPAdes
  3. Sorts assemblies by ALE score
  4. Merges the two best assemblies with GAM-NGS

For long reads (PacBio or Nanopore): Assembles with MiniASM

I could generate a pull request. I see multiple GenomeAssemblyHelp.html files, and I'm not sure which ones are auto generated.

levinas commented 8 years ago

Also plx.h5 and bax.h5 pacbio raw read files are now supported. FASTA and FASTQ files are automatically checked to see if they contain long reads.

levinas commented 8 years ago

Created pull request: https://github.com/dmachi/p3-web/pull/44 Andrew is going to deploy this on both prod and beta.

aswarren commented 8 years ago

Deployed

rkenyon commented 8 years ago

Service and UI are deployed, doing some testing.