Monday, April 3, 2023

Responses to question about functional annotation of metagenomic reads


Posted a question to a few places


Humann suggestion


 







fraggenescan on the raw reads, then use hmmer w/ pfam-A or kegg hmm.








EggNog Mapper








MGRAST

http://mgrast.org








Metawrap






Yooseph approach


https://pubmed.ncbi.nlm.nih.gov/27400380/

https://pubmed.ncbi.nlm.nih.gov/27585568/








mi-faser

https://bromberglab.org/project/mifaser/…










MGX

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0460-1…







MMseqs or Diamond







Squeeze Meta

https://github.com/jtamames/SqueezeMeta










Metageni/Superfocus

https://github.com/metageni/SUPER-FOCUS












Plass

https://github.com/metageni/SUPER-FOCUS











Megan + Diamond

https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.59







MetAnnotate

https://github.com/MetAnnotate/MetAnnotate









Review of relevance

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6289-6










UPROC

https://pubmed.ncbi.nlm.nih.gov/25540185/







Looking Glass

https://www.nature.com/articles/s41467-022-30070-8










Shortbred




Proteinfer / MGnify

https://www.ebi.ac.uk/metagenomics/pipelines/2.0





AntiSmash
















MMseq2








Sunday, June 15, 2014

Hawk moths in my yard in #DavisCA

Just a few pics I got tonight ... finally learning how to use my flash.










Photos taken with a Nikon D90 camera, Speedlight SB-910 flash and a Nikkor AF-S 105 mm Micro lens.

Sunday, May 25, 2014

Local elections in Davis, Yolo County and California are apparently a way for junk mail to be distributed. What a waste.

Well, the local elections in Davis, Yolo County and California are as far as I can tell mostly a way for junk mail to be distributed. What a waste.

Monday, January 6, 2014

Yolo Basin 1-6 - yellowthroat, sora, and more

Another good day at Yolo Basin.  Here are a few pics.