GSS_ATL

Genome Survey Sequencing in the Alligator Snapping Turtle

Reads Quality Control (fastp)

fastp -i SRR13329724_1.fastq.gz -I SRR13329724_2.fastq.gz -o fastpSRR13329724_1.fastq.gz -O fastpSRR13329724_2.fastq.gz

Reads Decontamination (Kraken2)

kraken2 --use-names --db /home/ant/kraken2-microbial-fatfree/ --gzip-compressed --paired fastpSRR13329724_1.fastq.gz fastpSRR13329724_2.fastq.gz --threads 11 --unclassified-out uncseqs#.fastq --report kraken2_report.txt --output kraken2_output.txt

Genome Size (KMC k-mer counting)

kmc -k21 -t11 -m64 -ci1 -cs100000 @FILES reads /home/ant/Turtle kmc_tools transform reads histogram reads21.histo -cx100000

Genome Size (RESPECT genome size estimation)

respect -d dataTURTLE/ -I dataTURTLE/hist_info.txt -N 11 --debug

Repetitive Element Analyses

RepeatExplorer

http://repeatexplorer.org/

DnaPipeTE

famdb.py -i Dfam.h5 families -f fasta_name -a -d Vertebrata --include-class-in-name > library14.fasta singularity shell --bind ~/dnaPipeTE/Project2:/mnt ~/dnaPipeTE/dnapipete.img cd /opt/dnaPipeTE python3 dnaPipeTE.py -input /mnt/data/fastpuncseqsMITONOTmapped.1.fastq.gz -output /mnt/dnaPipeTE_proj3 -genome_size 3000000000 -genome_coverage 0.20 -sample_number 2 -RM_lib /mnt/data/library14.fasta -RM_t 0.25 -cpu 12

EDTA

perl ../EDTA.pl --genome Shovill.fasta --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 --force 1

Mitochondrial Genome Assembly (GetOrganelle)

get_organelle_from_reads.py -1 SRR13329724_1.fastq.gz -2 SRR13329724_2.fastq.gz -t 11 -o SnappingTurtle.mitogenome -F animal_mt -R 10 -s SeedMitogemome.fasta

Mitochondrial Genome Annotation

https://baezaantonio.wixsite.com/clemsonmitogenomics/resources