Composition analysis of a Poolepynten ursus maritimus ancient sample

Download:

git clone https://github.com/pratas/bear.git
cd bear/

Download a build PUM:

chmod +x *.sh
./GetBear.sh
gunzip *.gz
./Trim.sh

Build the database (DB):

chmod +x *.sh
perl DownloadViruses.pl
perl DownloadArchaea.pl
perl DownloadBacteria.pl
perl DownloadFungi.pl
./DownloadMTV2.sh
./DownloadPlastidV2.sh
cat viruses.fa bacteria.fa archaea.fa fungi.fa mito.fna plast.fna | tr ' ' '_' \
| ./goose-extractreadbypattern complete_genome > DB.fa

Run metagenomic analysis:

./runIndividual.sh

Ancient DNA authentication scripts:

./runAuthCHIV14.sh               
./runAuthGeobacillus.sh  
./runAuthUrsus.sh
./runAuthCarrot.sh               
./runAuthTomato.sh
./runAuthHaloTrap.sh     
./runAuthCutibacterium.sh        
./runAuthRetrovirus.sh
./runAuthFlavobacteriumPhage.sh  

Attention: external links, namely from NCBI repositories, may be broken with time, although they are easily fixed.

Dependencies:

FALCON
AdapterRemoval
KESTREL
GULL
GOOSE
GeCo

Although they are installed and used automatically.

License is GPLv3.