Author: Meixi Lin
Date: November 2018
This is a repo using a combination of anacapa
and obitools
to generate taxonomical classification for some NGS sequences.
- move files: copy_rename_seq_10292018.sh
- qc and demultiplex using anacapa: anacapa_qc_dada2_qsub.sh
- ecotag classification:
- build & clean ref database:
- run classification: obitools_on_qcoutput_10302018.sh
- anacapa classification:
- build
crux
database: build_crux_db_MAMM2.sh & a similar one - create symlink for database used: create_symlink_crux_db.sh
- run classification: anacapa_classifier_qsub.sh
- build
please refer to the config file
- for obitools: https://git.metabarcoding.org/explore/projects
- for anacapa: https://github.com/limey-bean/Anacapa
Date: 11/27/2018
Remember to set BLCAperMINlen="0.8"
in the anacapa_vars.sh
In QC part
-m 30
instead of default -m 100
, here the minimum length after quality trimming is 30
instead of 100
.
In run_bowtie2_blca.sh
-b
percent similarity == 0.8 (this is default)
-p
percent length match == 0.8 (this is default)
In
sequence similarity cutoff is 0.95
- The CO1 was full length compared to default half-length
- The length cutoff set for 12SV5 resulted in that some shorter sequences (e.g. 10 bps) were analyzed and the sequences were assigned taxonomy. these sequences need to be out.