JAMP
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VascoElbrecht
JAMP - Just Another Metabarcoding Pipeline
alignment score too low, or score drop too high, vsearch v2.19.0_macos_aarch64 Need to check setting changes
need to do a few tests here
Hi Vasco, in some rare cases the Cutadapt function will run into an infinite xlim error, even though the data handling completed successfully. Got it worked around by commenting out...
I am trying to install JAMP in a virtual linux machine and I get this error: * installing to library ‘/usr/local/lib/R/site-library’ ERROR: dependency ‘seqinr’ is not available for package ‘JAMP’...
[input+output.zip](https://github.com/VascoElbrecht/JAMP/files/4426377/input%2Boutput.zip) + New option to use output from Bold identification with Species Level Barcode Records database by setting `db = "sp"`. With default options ( `db="all"` ) it should work...
Cluster ESVs to reduce table size and be better than OTU clustering allone = )
cat command can't handle more than 1000 files at once. Temporally fixed, for up to 2000 files.
Using rvest and extracting html information directly, compared to copy-pasting and smart grepping.
Relevant for servers / large datasets https://www.r-bloggers.com/long-running-r-commands-unix-screen-nohup-and-r/