Rebinning-Sediment-MG-merge-profiles

Objective: Continue with Anvio protocol for binning metagenomes

##SetUp

Base Directory (in cologn):

cd /opt/extern/bremen/symbiosis/sogin/prj001-comp-gene-chr
conda activate anvio-7

Notes from last time:

The anvi-profile function seems to have worked and we now have profile data for each library in the 02_Analysis folder.

  1. Merge anvi profiles One issue: I forgot to assign a sample name to the profile database

base script to change:

anvi-db-info in_I/PROFILE.db --self-key sample_id \
                                     --self-value "in_I" \
                                     --just-do-it

#check if it worked
anvi-db-info edge_E/PROFILE.db

anvi-merge */PROFILE.db -o SAMPLES-MERGED -c contigs.db
  1. Cluster contigs with automatic binning pipelines

Metabat cite: Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. 2019. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7:e7359 https://doi.org/10.7717/peerj.7359

## metabat2
anvi-cluster-contigs -p SAMPLES-MERGED/PROFILE.db -c contigs.db -C METABAT2 --driver metabat2 -m 2000 --seed 45 --just-do-it -T 24;

Concact

## Concact
anvi-cluster-contigs -p SAMPLES-MERGED/PROFILE.db -c contigs.db -C CONCOCT --driver concoct --just-do-it -T 24 --seed 45;

MaxBin

## Concact
anvi-cluster-contigs -p SAMPLES-MERGED/PROFILE.db -c contigs.db -C MAXBIN --driver maxbin2 --just-do-it -T 24;

Binsanity

## Concact
anvi-cluster-contigs -p SAMPLES-MERGED/PROFILE.db -c contigs.db -C MAXBIN --driver maxbin2 --just-do-it -T 24;

DasTool

Written on September 17, 2021