update documentation #8
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README.md
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| # The Metatranscriptome Assembly Pipeline | |||
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| ## Summary | |||
| This workflow is developed by Brian Foster at JGI. Original repo can be found [here](https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/tree/master/metatranscriptome). This workflow uses BBTools and SPAdes to assemble QC'ed transcriptomic reads. | |||
| This workflow was developed by Brian Foster at JGI. Original repo can be found (here)[https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/tree/master/metatranscriptome]. This workflow uses BBTools and SPAdes to assemble QC'ed transcriptomic reads. | |||
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check with Brian F., this is out of date since isn't on spades version 4.
README.md
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| # The Metatranscriptome Assembly Pipeline | |||
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| ## Summary | |||
| This workflow is developed by Brian Foster at JGI. Original repo can be found [here](https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/tree/master/metatranscriptome). This workflow uses BBTools and SPAdes to assemble QC'ed transcriptomic reads. | |||
| This workflow was developed by Brian Foster at JGI. Original repo can be found (here)[https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/tree/master/metatranscriptome]. This workflow uses BBTools and SPAdes to assemble QC'ed transcriptomic reads. | |||
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I was suprised that the end to end workflow doesn't include read qc? |
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the scripts that are run are |
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They aren't but this is an oversight IMO. The end to end metagenome workflow contains a filtering step https://github.com/microbiomedata/metaG/blob/main/nmdc-metag_full.wdl (call rqc.jgi_rqcfilter on line 26). The metaT end to end workflow should mirror this and have a filtering (read qc) step. |
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is readsqc not enough to count towards that? this is the assembly ticket? |
added image and updated index.rst