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lorentzben / visualize-ampliseq

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visualize-ampliseq

A pipeline built using DSL2 and nextflow to visualize the output from a nf-core/ampliseq analysis.

Example Parameters:

Only select the text to the left of the pipe (|) character 

# paramfile.yaml

input: "/cycle-4/litter-srs" | result directory absolute path from nf-core/ampliseq 
ioi: "Treatment" | "item of interest" column located in metadata that comparisions will be based on
metadata: "/cycle-4/litter-srs/metadata.tsv" | absolute filepath to metadata file from nf-core/ampliseq analysis
outdir: "/cycle-4/litter-srs-nc-mock-16500-with-viz" | outdir of this analysis where resultfiles will be published
ordioi: "/cycle-4/litter/ord_ioi.csv" | "ordered item of interest" if you prefer a sepecific ordering control vs treatment
rare: 16500 | rarefaction depth can be determined by examining rarefaction/srs curve
srs: true | does SRS need to be utilized?
negative: "NC" | what is the value of negative controls in your ioi col
mock: "MOCK" | what is the value of positive control/mock community in your ioi col
refSeq: "/reference-community/atcc_20_ref.qza" | reference sequences for your mock community in qza format, see below
refTab: "/reference-community/expected-taxonomy.qza" | reference abundances for mock community in qza format, see below

To run:

One note I suggest is to put the command below and the paramfile in a git repository and log commits as you change paramters for reproducibility 


$ ml Nextflow/22.04.5

# To run on a slurm server with singularity and using the paramfile above

$ nextflow run lorentzben/visualize-ampliseq \
    -r 2.0 \
    -with-tower \
    -profile slurm,singularity \
    -params-file paramfile.yaml \
    -latest \
    -resume

# To run on a local machine with docker and using the paramfile above

$ nextflow run lorentzben/visualize-ampliseq \
    -r 2.0 \
    -with-tower \
    -profile local,docker \
    -params-file paramfile.yaml \
    -latest \
    -resume

RefSeq

If you have a directory of sequences you can use the following command:

$ cd /reference-community
$ cat *.fasta > atcc_20_ref.fasta
$ head /reference-community/atcc_20_ref.fasta

$ qiime tools import \
  --input-path /reference-community/atcc_20_ref.fasta \
  --output-path /reference-community/atcc_20_ref.qza \
  --type 'FeatureData[Sequence]'

RefTab


$ nano reftab.tsv

Taxonomy        MOCK167 MOCK288 MOCK323 MOCK71
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Pseudomonadales;D_4__Moraxellaceae;D_5__Acinetobacter;D_6__baumannii    0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Bacillales;D_4__Bacillaceae;D_5__Bacillus;D_6__pacificus        0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Pseudomonadales;D_4__Moraxellaceae;D_5__Acinetobacter;__        0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Actinobacteriota;D_2__Actinobacteria;D_3__Bifidobacteriales;D_4__Bifidobacteriaceae;D_5__Bifidobacterium;D_6__adolescentis   0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Clostridiaceae;D_5__Clostridium sensu stricto 1;D_6__beijerinckii 0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Actinobacteriota;D_2__Actinobacteria;D_3__Propionibacteriales;D_4__Propionibacteriaceae;D_5__Cutibacterium;D_6__acnes        0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Deinococcota;D_2__Deinococci;D_3__Deinococcales;D_4__Deinococcaceae;D_5__Deinococcus;D_6__radiodurans R1     0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Lactobacillales;D_4__Enterococcaceae;D_5__Enterococcus;D_6__faecalis    0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Enterobacterales;D_4__Enterobacteriaceae;D_5__Escherichia-Shigella;D_6__coli    0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Campylobacterota;D_2__Campylobacteria;D_3__Campylobacterales;D_4__Helicobacteraceae;D_5__Helicobacter;D_6__pylori    0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Lactobacillales;D_4__Lactobacillaceae;D_5__Lactobacillus;D_6__gasseri   0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Burkholderiales;D_4__Neisseriaceae;D_5__Neisseria;D_6__meningitidis     0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Bacteroidota;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Porphyromonadaceae;D_5__Porphyromonas;D_6__gingivalis  0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Pseudomonadales;D_4__Pseudomonadaceae;D_5__Pseudomonas;__       0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Rhodobacterales;D_4__Rhodobacteraceae;D_5__Cereibacter;__       0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Actinobacteriota;D_2__Actinobacteria;D_3__Actinomycetales;D_4__Actinomycetaceae;D_5__Actinomyces;D_6__odontolytica   0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Staphylococcales;D_4__Staphylococcaceae;D_5__Staphylococcus;D_6__aureus 0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Staphylococcales;D_4__Staphylococcaceae;D_5__Staphylococcus;D_6__epidermidis    0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Lactobacillales;D_4__Streptococcaceae;D_5__Streptococcus;D_6__agalactiae        0.05    0.05    0.05    0.05
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Lactobacillales;D_4__Streptococcaceae;D_5__Streptococcus;D_6__mutans    0.05    0.05    0.05    0.05

Taking in the file reftab.tsv you can generate the qza you need as below. You must ensure that your mock community IDs and names are the same or you will get an issue. 


$ biom convert \
  -i reftab.tsv \
  -o expected-taxonomy.biom \
  --table-type="OTU table" \
  --to-json

$ qiime tools import \
 --type FeatureTable[RelativeFrequency] \
 --input-path expected-taxonomy.biom \
 --input-format BIOMV100Format \
 --output-path /reference-community/expected-taxonomy.qza