Difference between revisions of "Kaiju"

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= assembly statistics =
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=annotation of the assembly with prokka =
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= annotation of the assembly with prokka version 1.11 =
 
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* directiory: <tt>2018_03_02_Syngnamydia_salmonis/2018_03_02_annotation_initial_assembly</tt>
 
−
 
 
 
     prokka --locustag SYSA --genus Syngnamydia --species salmonis --strain 4K220114E9 --compliant --centre CHUV Genome_Syngnamydia_4K220114E9.fasta
 
     prokka --locustag SYSA --genus Syngnamydia --species salmonis --strain 4K220114E9 --compliant --centre CHUV Genome_Syngnamydia_4K220114E9.fasta
  
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= kaiju =
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=kaiju=
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* directory: <tt>2018_03_02_Syngnamydia_salmonis/2018_03_23_kaiju_initial_assembly</tt>
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==Setup of kaiju database (progenomes)==
  
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== setup of kaiju database (progenomes) ==
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*see https://github.com/bioinformatics-centre/kaiju
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* see https://github.com/bioinformatics-centre/kaiju
 
  
 
     # Representative genomes from proGenomes
 
     # Representative genomes from proGenomes
 
     makeDB.sh -p
 
     makeDB.sh -p
  
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== compare faa file to kaiju database ==
+
==Sompare faa file to kaiju database==
 
     kaiju -t ../progenomes/nodes.dmp -f ../progenomes/kaiju_db.fmi -i PROKKA_03062018.faa -p > output.txt
 
     kaiju -t ../progenomes/nodes.dmp -f ../progenomes/kaiju_db.fmi -i PROKKA_03062018.faa -p > output.txt
  
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== generate summary file ==
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==Generate summary file==
 
     kaijuReport -i output.txt -o report.tab -t ../progenomes/nodes.dmp -n ../progenomes/names.dmp -r phylum
 
     kaijuReport -i output.txt -o report.tab -t ../progenomes/nodes.dmp -n ../progenomes/names.dmp -r phylum
  
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==Generate summary file to use for circos==
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== generate summary file to use for circos ==
 
 
     addTaxonNames -t nodes.dmp -n names.dmp -i output.txt -o locus_taxonomy.tab -r phylum
 
     addTaxonNames -t nodes.dmp -n names.dmp -i output.txt -o locus_taxonomy.tab -r phylum
  
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* <tt>locus_taxonomy.tab</tt> is a two colum file with: locus tag, phylum\_name
+
*<tt>locus_taxonomy.tab</tt> is a two colum file with: locus tag, phylum\_name
  
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* need to be manually edited to add target phylum of interest (max 2, see below)
+
*need to be manually edited to add target phylum of interest (max 2, see below)
−
 
 
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= self mapping & mummer2circos =
 
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== execution ==
 
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* directory: <tt>2018_03_02_Syngnamydia_salmonis/2018_03_02_self_mapping_initial_assembly</tt>
 
  
 +
=Self mapping & mummer2circos=
 +
==Execution (bbmap)==
 
     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
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<p class="verse">
 
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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<br />
 
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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<br />
 
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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]<br />
 
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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]<br />
 
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<br />
 
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Retaining first best site only for ambiguous mappings.<br />
 
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NOTE: Ignoring reference file because it already appears to have been processed.<br />
 
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NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt<br />
 
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Set genome to 1<br />
 
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<br />
 
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Loaded Reference: 0.187 seconds.<br />
 
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Loading index for chunk 1-1, build 1<br />
 
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Generated Index: 0.777 seconds.<br />
 
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Analyzed Index:  1.953 seconds.<br />
 
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Found samtools 1.7<br />
 
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Started output stream: 0.107 seconds.<br />
 
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Cleared Memory:    0.149 seconds.<br />
 
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Processing reads in paired-ended mode.<br />
 
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Started read stream.<br />
 
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Started 4 mapping threads.<br />
 
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Detecting finished threads: 0, 1, 2, 3<br />
 
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<br />
 
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&#xa0;&#xa0;&#xa0;-------------&#x2013;&#x2014;  Results  -------------&#x2013;&#x2014;<br />
 
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<br />
 
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Genome:                1<br />
 
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Key Length:            13<br />
 
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Max Indel:            16000<br />
 
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Minimum Score Ratio:  0.56<br />
 
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Mapping Mode:        normal<br />
 
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Reads Used:          80051666 (10086509916 bases)<br />
 
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<br />
 
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Mapping:          1740.577 seconds.<br />
 
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Reads/sec:      45991.45<br />
 
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kBases/sec:      5794.92<br />
 
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<br />
 
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<br />
 
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Pairing data:  pct pairs num pairs pct bases   num bases<br />
 
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<br />
 
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mated pairs:      6.3830%   2554856   6.3830%   643823712<br />
 
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bad pairs:        0.5098%   204058   0.5098%     51422616<br />
 
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insert size avg:   572.74<br />
 
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<br />
 
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<br />
 
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Read 1 data:      pct reads num reads pct bases   num bases<br />
 
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<br />
 
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mapped:            7.3722%   2950781   7.3722%   371798406<br />
 
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unambiguous:      7.3702%   2949974   7.3702%   371696724<br />
 
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ambiguous:        0.0020%       807   0.0020%       101682<br />
 
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low-Q discards:    0.0000%         4   0.0000%         504<br />
 
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<br />
 
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perfect best site:   6.4366%   2576300   6.4366%   324613800<br />
 
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semiperfect site:   6.4476%   2580705   6.4476%   325168830<br />
 
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rescued:          0.0508%     20325<br />
 
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<br />
 
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Match Rate:            NA       NA 96.1995%   368304608<br />
 
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Error Rate:      12.3749%   365158   3.7573%     14384862<br />
 
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Sub Rate:        12.0228%   354768   0.6510%     2492378<br />
 
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Del Rate:          1.7929%     52906   2.8880%     11056739<br />
 
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Ins Rate:          2.6004%     76731   0.2183%       835745<br />
 
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N Rate:            0.7226%     21323   0.0433%       165675<br />
 
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<br />
 
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<br />
 
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Read 2 data:      pct reads num reads pct bases   num bases<br />
 
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<br />
 
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mapped:            7.1449%   2859815   7.1449%   360336690<br />
 
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unambiguous:      7.1430%   2859047   7.1430%   360239922<br />
 
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ambiguous:        0.0019%       768   0.0019%       96768<br />
 
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low-Q discards:    0.1894%     75803   0.1894%     9551178<br />
 
−
<br />
 
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perfect best site:   5.6690%   2269075   5.6690%   285903450<br />
 
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semiperfect site:   5.6785%   2272877   5.6785%   286382502<br />
 
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rescued:          0.0736%     29444<br />
 
−
<br />
 
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Match Rate:            NA       NA 95.1404%   355147035<br />
 
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Error Rate:      20.5184%   586790   4.8208%     17995311<br />
 
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Sub Rate:        20.2023%   577748   1.1375%     4246210<br />
 
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Del Rate:          1.7640%     50448   3.4693%     12950466<br />
 
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Ins Rate:          2.5537%     73030   0.2139%       798635<br />
 
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N Rate:            0.5302%     15164   0.0388%       144810<br />
 
−
<br />
 
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Total time:    1743.960 seconds.<br />
 
−
</p>
 
  
 
     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
 
     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
  
−
* <tt>-lt</tt> allow to color CDS based on a taxon table of the followinf format
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*<tt>-lt</tt> allow to color CDS based on a taxon table of the followinf format
−
 
+
*
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<p class="verse">
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<syntaxhighlight lang="bash">
−
#Chlamydiae<br />
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#Chlamydiae
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\\#Bacteroidetes<br />
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#Bacteroidetes
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SYSA\_00001<br />
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SYSA_00001
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SYSA\_00002 Chlamydiae<br />
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SYSA_00002 Chlamydiae
−
SYSA\_00003 Chlamydiae<br />
+
SYSA_00003 Chlamydiae
−
SYSA\_00004 Chlamydiae<br />
+
SYSA_00004 Chlamydiae
 +
</syntaxhighlight><br />
 
</p>
 
</p>
  
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* the 2 first lines indicates the taxon to color (with #)
+
*the 2 first lines indicates the taxon to color (with #)
  
−
* the folowing lines indocates the taxonomy of each locus
+
*the folowing lines indocates the taxonomy of each locus

Latest revision as of 22:10, 30 January 2019

annotation of the assembly with prokka

   prokka --locustag SYSA --genus Syngnamydia --species salmonis --strain 4K220114E9 --compliant --centre CHUV Genome_Syngnamydia_4K220114E9.fasta

kaiju

Setup of kaiju database (progenomes)

   # Representative genomes from proGenomes
   makeDB.sh -p

Sompare 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 (bbmap)

   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

   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
#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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