06_Workshop.md

Workshop

Charts

• Brucellosis LMN01 HTML
• Plague Black Death SVG
• Plague Black Death HTML
  • Max Depth: 7
  • Font Size: 40
• Plague Pre-Justinian SVG
• Plague Pre-Justinian HTML
  • Max Depth: 7
  • Font Size: 25

Analysis

Plague (Black Death)

1. Convert to fasta.

   samtools fasta Yersinia_pestis_Black-Death-8291.bam > Yersinia_pestis_Black-Death-8291.fasta

2. Taxonomic classification with Kraken.

   $ /home/keaton/Projects/Plague/YorkBarbican/envs/kraken2/bin/kraken2 \
       --db /2/scratch/keaton/kraken2-microbial-fatfree/ \
       --threads 10 \
       --confidence 0.2  \
       --report-minimizer-data \
       --minimum-hit-groups 2 \
       --output kraken2/Yersinia_pestis_Black-Death-8291.output \
       --report kraken2/Yersinia_pestis_Black-Death-8291.report \
       data/Yersinia_pestis_Black-Death-8291.fasta
   
   9776505 sequences (535.46 Mbp) processed in 7.526s (77936.7 Kseq/m, 4268.62 Mbp/m).
   7012387 sequences classified (71.73%)
   2764118 sequences unclassified (28.27%)

3. Krona chart creation.

   # Krona text
   $ cut \
       -f 2,3 \
       kraken2/Yersinia_pestis_Black-Death-8291.output \
       > kraken2/Yersinia_pestis_Black-Death-8291.krona
   
   # Krona html
   $ /home/keaton/myapps/KronaTools-2.8/bin/ktImportTaxonomy \
       -i \
       -k \
       -o kraken2/Yersinia_pestis_Black-Death-8291.krona.html \
       -tax /home/keaton/database/Krona/taxonomy-2019-12-16/ \
       kraken2/Yersinia_pestis_Black-Death-8291.krona
   
   Loading taxonomy...
   Importing kraken2/Yersinia_pestis_Black-Death-8291.krona...
   [ WARNING ]  The following taxonomy IDs were not found in the local database and were set to root (if they were recently added to NCBI, use updateTaxonomy.sh to update the local
                   database): 1743172 2109625 1049581 1981981 644968 2036817 2183547 1826873 134962 2071623
   Writing kraken2/Yersinia_pestis_Black-Death-8291.krona.html...
   [ WARNING ]  Too many query IDs to store in chart; storing supplemental files in 'kraken2/Yersinia_pestis_Black-Death-8291.krona.html.files'.        

Plague (Pre-Justinian)

• BioSample: SAMEA1061800
• Strain: DA101
• DOI: https://doi.org/10.1038/s41586-018-0094-2

1. Convert to fasta.

   samtools fasta Yersinia_pestis_Pre-Justinian-DA101.bam > Yersinia_pestis_Pre-Justinian-DA101.fasta

2. Taxonomic classification with Kraken.

   $ /home/keaton/Projects/Plague/YorkBarbican/envs/kraken2/bin/kraken2 \
   --db /2/scratch/keaton/kraken2-microbial-fatfree/ \
   --threads 10 \
   --confidence 0.2  \
   --report-minimizer-data \
   --minimum-hit-groups 2 \
   --output kraken2/Yersinia_pestis_Pre-Justinian-DA101.output \
   --report kraken2/Yersinia_pestis_Pre-Justinian-DA101.report \
   data/Yersinia_pestis_Pre-Justinian-DA101.fasta
   
   Loading database information... done.
   10086461 sequences (619.14 Mbp) processed in 10.512s (57573.6 Kseq/m, 3534.03 Mbp/m).
   477198 sequences classified (4.73%)
   9609263 sequences unclassified (95.27%)

3. Krona chart creation.

   # Krona text
   $ cut \
       -f 2,3 \
       kraken2/Yersinia_pestis_Pre-Justinian-DA101.output \
       > kraken2/Yersinia_pestis_Pre-Justinian-DA101.krona
   
   # Krona html
   $ /home/keaton/myapps/KronaTools-2.8/bin/ktImportTaxonomy \
       -i \
       -k \
       -o kraken2/Yersinia_pestis_Pre-Justinian-DA101.krona.html \
       -tax /home/keaton/database/Krona/taxonomy-2019-12-16/ \
       kraken2/Yersinia_pestis_Pre-Justinian-DA101.krona
   
   Loading taxonomy...
   Importing kraken2/Yersinia_pestis_Pre-Justinian-DA101.krona...
   [ WARNING ]  The following taxonomy IDs were not found in the local database and were set to root (if they were recently added to NCBI, use updateTaxonomy.sh to update
                   the local database): 2171980 2109625 134962 443255 2183547 2036817 330 62153
   Writing kraken2/Yersinia_pestis_Pre-Justinian-DA101.krona.html...
   [ WARNING ]  Too many query IDs to store in chart; storing supplemental files in 'kraken2/Yersinia_pestis_Pre-Justinian-DA101.krona.html.files'.

Plague (Justinian)

• BioSample: SAMN02442693
• Strain: A120
• DOI: https://doi.org/10.1016/S1473-3099(13)70323-2

1. Convert to fasta.

   samtools fasta Yersinia_pestis_Justinian-A120.bam > Yersinia_pestis_Justinian-A120.fasta

2. Taxonomic classification with Kraken.

   $ /home/keaton/Projects/Plague/YorkBarbican/envs/kraken2/bin/kraken2 \
   --db /2/scratch/keaton/kraken2-microbial-fatfree/ \
   --threads 10 \
   --confidence 0.2  \
   --report-minimizer-data \
   --minimum-hit-groups 2 \
   --output kraken2/Yersinia_pestis_Justinian-A120.output \
   --report kraken2/Yersinia_pestis_Justinian-A120.report \
   data/Yersinia_pestis_Justinian-A120.fasta
   
   Loading database information... done.
   10086461 sequences (619.14 Mbp) processed in 10.512s (57573.6 Kseq/m, 3534.03 Mbp/m).
   477198 sequences classified (4.73%)
   9609263 sequences unclassified (95.27%)