benkaehler/readytowear

Ready-made Taxonomic Weights Repository

readytowear's Issues

Write readme tutorial

the tutorial should cover:

1. how to use the readytowear weights
2. how to contribute new readytowear fashions

Updating the default V4 EMP primers

Just noticed that the V4 primers being used in the weight assembly scripts are using the old EMP primers (ex here). A few years back these were modified slightly and degeneracy added (as described here). I'm not sure if this would have any real significant effect but might be worth updating nevertheless.

Primers currently being used in weight assembly:
FWD: GTGCCAGCMGCCGCGGTAA
REV: GGACTACHVGGGTWTCTAAT

Recommended update to new EMP primers:
FWD: GTGYCAGCMGCCGCGGTAA;
REV: GGACTACNVGGGTWTCTAAT

Add SILVA 138.1 weights

We only have version 138 weights. 138.1 has been requested...

Clarification: GTDB mixed orientation warning only applies to full length refs?

Howdy!

I noticed the disclaimer on the GTDB data page:

Warning: files in this directory are experimental. Many of the reference sequences appear to be in mixed orientations, which currently are not handled well by q2-feature-classifier and may yield misleading results. Use at your own risk.

Which is of course a valid concern, but this only applies to the full length refs, right? Since the V4 ones go through the extract read process initially which correct these mixed orientations? (as per @nbokulich's note here).
Or... does extract read's --p-read-orientation both only apply both orientation in its search and doesn't actually correct the reads in the output?

Thanks!

Asking about animal-proximal-gut.qza

Hello, I'm Hanbeen Kim.

Thank you for being so dedicated.

I have a question about "animal-proximal-gut" database.

I have studied the rumen microbiome and tried to make a weighted classifier.

Does the "animal-proximal-gut" mean rumen?

If it is not, can you advise how to make a specific database to make a weighted classifier?

I hope you have a nice day.

Hanbeen Kim.

Compatibility of silva v138.1 with class-weights based on v138

Hi, is it possible to use silva v138.1 reference seqs and taxonomies together with class-weights available in your readytowear inventory, which are based on v138?
Thanks for this great tools!

Issues reading ref-seqs.qza in QIIME2

Hello, I downloaded ref-seqs.qza using the following command:

wget -O "ref-seqs.qza" "https://github.com/BenKaehler/readytowear/blob/master/data/gg_13_8/515f-806r/ref-seqs.qza"

Then I tried running it as part of the command:

qiime feature-classifier fit-classifier-naive-bayes \
    --i-reference-reads ref-seqs.qza  \
    --i-reference-taxonomy ref-tax.qza \
    --i-class-weight human-stool.qza \
    --o-classifier gg138_v4_human-stool_classifier.qza

And got the following error: " (1/1) Invalid value for '--i-reference-reads': ref-seqs.qza is not a QIIME archive."

I tried viewing the object using qiime tools peek ref-seqs.qza and got a similar error:
"raise ValueError("%s is not a QIIME archive." % filepath)
ValueError: ref-seqs.qza is not a QIIME archive."

Interestingly, when I downloaded the file in my browser and tried viewing it on the QIIME2 website it was able to interpret it ("DNASequencesDirectoryFormat" format file of type "FeatureData[Sequence]"). Do you have any idea what might be going wrong or if there is something wrong with the file? Thanks!

Plant datasets

Hello there,
Quick questions,

1. when it says plant corpus, does it refer to the whole plant or some specific parts (I have a leaf and root 16s amplicons);
2. Is it possible to combine two or more datasets into something more comprenhensive?

Cheers,
Luis Alfonso.

Update GTDB Release

The GTDB release is getting a bit long in the tooth. We’re now two releases out of date.

Taxonomic weight for animal fecal samples

Hoping you can help clarify which taxonomic weight .qza file to use for mouse fecal samples. Animal-distal-gut or animal-secretion?

Scripts needed for human vaginal weights.

PR #8 did not include scripts for generating the human vaginal weights.

Those scripts must be added.

Animals in animal-distal-gut?

Hello,

I am doing microbiome analysis on samples from tenrecs. I am curious what animals are represented by the animal distal gut weights and if you think this file would be appropriate to use on my samples since the tenrec group is likely poorly represented in reference databases.

Thank you!

add an inventory

searchable inventory of readytowear weights, listing:
name (sample type)
reference database
primers
redbiom search terms?

see mockrobiota for an example

Also include a script to generate this inventory.

Write some CI

Would be good if we could automate checking that the weights and uploaded references can be used to build valid classifiers.