Tpillone at 22:10, 30 January 2019

2019-01-30T22:10:14Z

Tpillone: Created page with " = assembly statistics = {| class=wikitable |- |n |n:1000 |n:N50 |min |median |mean |N50 |max |sum | |- |- |15 |15 |4 |31206 |120770 |143557 |210012 |531893 |2153..."

2019-01-30T22:06:00Z

Created page with " = assembly statistics = {| class=wikitable |- |n |n:1000 |n:N50 |min |median |mean |N50 |max |sum | |- |- |15 |15 |4 |31206 |120770 |143557 |210012 |531893 |2153..."

New page

= assembly statistics =
{| class=wikitable

|-
|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: <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

= kaiju =
* directory: <tt>2018_03_02_Syngnamydia_salmonis/2018_03_23_kaiju_initial_assembly</tt>

== setup of kaiju database (progenomes) ==
* see https://github.com/bioinformatics-centre/kaiju

# 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

{| class=wikitable

|-
|%
|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

* <tt>locus_taxonomy.tab</tt> 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: <tt>2018_03_02_Syngnamydia_salmonis/2018_03_02_self_mapping_initial_assembly</tt>

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

* <tt>-lt</tt> 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

Kaiju - Revision history

Tpillone at 22:10, 30 January 2019

Tpillone: Created page with " = assembly statistics = {| class=wikitable |- |n |n:1000 |n:N50 |min |median |mean |N50 |max |sum | |- |- |15 |15 |4 |31206 |120770 |143557 |210012 |531893 |2153..."