Kaiju

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assembly statistics

n n:1000 n:N50 min median mean N50 max sum
15 15 4 31206 120770 143557 210012 531893 2153368 Genome\_Syngnamydia\_4K22011

annotation of the assembly with prokka version 1.11

  • directiory: 2018_03_02_Syngnamydia_salmonis/2018_03_02_annotation_initial_assembly
   prokka --locustag SYSA --genus Syngnamydia --species salmonis --strain 4K220114E9 --compliant --centre CHUV Genome_Syngnamydia_4K220114E9.fasta

kaiju

  • directory: 2018_03_02_Syngnamydia_salmonis/2018_03_23_kaiju_initial_assembly

setup of kaiju database (progenomes)

   # Representative genomes from proGenomes
   makeDB.sh -p

compare faa file to kaiju database

   kaiju -t ../progenomes/nodes.dmp -f ../progenomes/kaiju_db.fmi -i PROKKA_03062018.faa -p > output.txt

generate summary file

   kaijuReport -i output.txt -o report.tab -t ../progenomes/nodes.dmp -n ../progenomes/names.dmp -r phylum
% reads phylum
44.844597 909 Chlamydiae
7.153429 145 Proteobacteria
3.404046 69 Firmicutes
3.157375 64 Bacteroidetes
1.184016 24 Actinobacteria
0.542674 11 Euryarchaeota
0.444006 9 Cyanobacteria
0.345338 7 Spirochaetes
0.246670 5 Verrucomicrobia
0.246670 5 Candidatus Cloacimonetes
0.197336 4 Deinococcus-Thermus
0.197336 4 Acidobacteria
0.197336 4 Chloroflexi
0.197336 4 Planctomycetes
0.148002 3 Thermodesulfobacteria
0.098668 2 Chlorobi
0.098668 2 Fusobacteria
0.098668 2 Thermotogae
0.098668 2 Balneolaeota
0.049334 1 Candidatus Aminicenantes
0.049334 1 Dictyoglomi
0.049334 1 Gemmatimonadetes
0.049334 1 Aquificae
0.049334 1 Deferribacteres
0.049334 1 Candidatus Poribacteria
0.049334 1 Synergistetes
0.049334 1 Tenericutes
0.049334 1 Thaumarchaeota
0.049334 1 Calditrichaeota
0.000000 0 Viruses
0.789344 16 cannot be assigned to a phylum
35.816479 726 unclassified


generate summary file to use for circos

   addTaxonNames -t nodes.dmp -n names.dmp -i output.txt -o locus_taxonomy.tab -r phylum
  • locus_taxonomy.tab is a two colum file with: locus tag, phylum\_name
  • need to be manually edited to add target phylum of interest (max 2, see below)

self mapping & mummer2circos

execution

  • directory: 2018_03_02_Syngnamydia_salmonis/2018_03_02_self_mapping_initial_assembly
   bbmap.sh ref=PROKKA_03022018.fna in1=4K220114E9DNA_CGGAGCCTCCTAGAGT_L002_R1_001_BHB2GGADXX.filt.fastq.gz in2=4K220114E9DNA_CGGAGCCTCCTAGAGT_L002_R2_001_BHB2GGADXX.filt.fastq.gz outm=bbmap_initial.bam

bbmap.sh ref=PROKKA\_03022018.fna in1=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R1\_001\_BHB2GGADXX.filt.fastq.gz in2=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R2\_001\_BHB2GGADXX.filt.fastq.gz outm=bbmap\_initial.bam
java -Djava.library.path=/home/tpillone/miniconda2/opt/bbmap-37.90/jni/ -ea -Xmx1561m -cp home/tpillone/miniconda2/opt/bbmap-37.90/current align2.BBMap build=1 overwrite=true fastareadlen=500 ref=PROKKA\_03022018.fna in1=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R1\_001\_BHB2GGADXX.filt.fastq.gz in2=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R2\_001\_BHB2GGADXX.filt.fastq.gz outm=bbmap\_initial.bam
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=PROKKA\_03022018.fna, in1=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R1\_001\_BHB2GGADXX.filt.fastq.gz, in2=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R2\_001\_BHB2GGADXX.filt.fastq.gz, outm=bbmap\_initial.bam]
Version 37.90 [build=1, overwrite=true, fastareadlen=500, ref=PROKKA\_03022018.fna, in1=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R1\_001\_BHB2GGADXX.filt.fastq.gz, in2=4K220114E9DNA\_CGGAGCCTCCTAGAGT\_L002\_R2\_001\_BHB2GGADXX.filt.fastq.gz, outm=bbmap\_initial.bam]

Retaining first best site only for ambiguous mappings.
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1

Loaded Reference: 0.187 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 0.777 seconds.
Analyzed Index: 1.953 seconds.
Found samtools 1.7
Started output stream: 0.107 seconds.
Cleared Memory: 0.149 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 4 mapping threads.
Detecting finished threads: 0, 1, 2, 3

   -------------–— Results -------------–—

Genome: 1
Key Length: 13
Max Indel: 16000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 80051666 (10086509916 bases)

Mapping: 1740.577 seconds.
Reads/sec: 45991.45
kBases/sec: 5794.92


Pairing data: pct pairs num pairs pct bases num bases

mated pairs: 6.3830% 2554856 6.3830% 643823712
bad pairs: 0.5098% 204058 0.5098% 51422616
insert size avg: 572.74


Read 1 data: pct reads num reads pct bases num bases

mapped: 7.3722% 2950781 7.3722% 371798406
unambiguous: 7.3702% 2949974 7.3702% 371696724
ambiguous: 0.0020% 807 0.0020% 101682
low-Q discards: 0.0000% 4 0.0000% 504

perfect best site: 6.4366% 2576300 6.4366% 324613800
semiperfect site: 6.4476% 2580705 6.4476% 325168830
rescued: 0.0508% 20325

Match Rate: NA NA 96.1995% 368304608
Error Rate: 12.3749% 365158 3.7573% 14384862
Sub Rate: 12.0228% 354768 0.6510% 2492378
Del Rate: 1.7929% 52906 2.8880% 11056739
Ins Rate: 2.6004% 76731 0.2183% 835745
N Rate: 0.7226% 21323 0.0433% 165675


Read 2 data: pct reads num reads pct bases num bases

mapped: 7.1449% 2859815 7.1449% 360336690
unambiguous: 7.1430% 2859047 7.1430% 360239922
ambiguous: 0.0019% 768 0.0019% 96768
low-Q discards: 0.1894% 75803 0.1894% 9551178

perfect best site: 5.6690% 2269075 5.6690% 285903450
semiperfect site: 5.6785% 2272877 5.6785% 286382502
rescued: 0.0736% 29444

Match Rate: NA NA 95.1404% 355147035
Error Rate: 20.5184% 586790 4.8208% 17995311
Sub Rate: 20.2023% 577748 1.1375% 4246210
Del Rate: 1.7640% 50448 3.4693% 12950466
Ins Rate: 2.5537% 73030 0.2139% 798635
N Rate: 0.5302% 15164 0.0388% 144810

Total time: 1743.960 seconds.

   mummer2circos.py -r PROKKA_03022018.fna -q GCF_000237205.1/GCF_000237205.1_ASM23720v1_genomic.fna jellyfish_metagenome/FLZN01000001.fna jellyfish_metagenome/FLZO01000001.fna jellyfish_metagenome/FUHP01000001.fna jellyfish_metagenome/OBEO01000001.fna GCF_000020225.1/GCF_000020225.1_ASM2022v1_genomic.fna GCF_000196115.1/GCF_000196115.1_ASM19611v1_genomic.fna -s PROKKA_03022018.depth -gb PROKKA_03022018.gbf -l -a promer -lt locus_taxonomy.tab
  • -lt allow to color CDS based on a taxon table of the followinf format

  1. Chlamydiae

\\#Bacteroidetes
SYSA\_00001
SYSA\_00002 Chlamydiae
SYSA\_00003 Chlamydiae
SYSA\_00004 Chlamydiae

  • the 2 first lines indicates the taxon to color (with #)
  • the folowing lines indocates the taxonomy of each locus
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