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[MRG] Clean up "introduction" text in docs - #1684
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| - counting k-mers and estimating data set coverage based on k-mer counts; | ||
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| - running Velvet and calculating assembly statistics; |
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Really? Is this still true?
| The most important thing to think about when using khmer is whether or not the transformation or filter you're applying is appropriate for the data you're trying to assemble. | ||
| For example, two of the most powerful operations available in khmer, graph-size filtering and graph partitioning, only make sense for assembly datasets with many theoretically unconnected components. | ||
| This is typical of metagenomic data sets. | ||
| Also, while digital normalization can be helpful for transcriptome *assembly*, it is inappropriate for other RNA-seq applications, such as differential expression analysis, that rely on signal from variable coverage. |
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| - optimizing assemblies on various parameters; | ||
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| - converting FASTQ to FASTA; |
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Could also mention interleaving/decoupling fastq.
Codecov Report
@@ Coverage Diff @@
## master #1684 +/- ##
==========================================
- Coverage 64.16% 64.16% -0.01%
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Files 79 79
Lines 12189 12188 -1
Branches 3072 3072
==========================================
- Hits 7821 7820 -1
- Misses 2670 2671 +1
+ Partials 1698 1697 -1
Continue to review full report at Codecov.
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This is ready for review. I'm guessing @ctb will want a crack at this. |
standage
changed the title
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*bump* |
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@betatim and @luizirber and I are going to hack a bit on khmer at PyCon (and @camillescott, if she's coming and interested). If @ctb has not reviewed this by then I'll recruit someone else to review this then. Hopefully we can check all of the remaining 2.1 release boxes before PyCon is over. |
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No specific sense of urgency, just didn't want the PR (and thus the release) to languish for an indeterminate amount of time. It can definitely wait until Saturday. :-) |
Doing my best to bring this up-to-date. See #853.
make testDid it pass the tests?changes were made?