My first blobplot

1. Create a blobDB file from input files

1.1 Input file requirements

• one assembly file, e.g. example/assembly.fna
• one (or more) coverage file(s) e.g. example/mapping_1.bam
• one (or more) hits file(s), e.g. example/blast.out

1.2 Creating a blobDB

# using the files provided in the test_files/ folder 
./blobtools create \
 -i example/assembly.fna \
 -b example/mapping_1.bam \
 -t example/blast.out \
 -o example/my_first_blobplot

2. Create a view of a blobDB file

2.1. Creating a view

• Using blobtools view, information stored in a blobDB can be extracted.
• Using the default settings, blobtools view will generate a tabular output for the taxonomic rank of "phylum".

./blobtools view \
 -i example/my_first_blobplot.blobDB.json \
 -o example/

2.2. Inspecting the output

• The resulting file can be inspected using a one-liner (to indent the columns properly), e.g.:

grep '^##' example/my_first_blobplot.blobDB.table.txt ; \
 grep -v '^##' example/my_first_blobplot.blobDB.table.txt | \
 column -t -s $'\t'

## blobtools v1.0
## assembly	: example/assembly.fna
## coverage	: bam0 - example/mapping_1.bam
## taxonomy	: tax0 - example/blast.out
## nodesDB	: data/nodesDB.txt
## taxrule	: bestsum
##
# name     length  GC      N  bam0     phylum.t.6      phylum.s.7  phylum.c.8
contig_1   756     0.2606  0  90.406   Actinobacteria  200.0       0
contig_2   1060    0.2623  0  168.409  Actinobacteria  2300.0      0
contig_3   602     0.2342  0  43.761   Actinobacteria  10000.0     0
contig_4   951     0.3155  0  456.313  Actinobacteria  1000.0      0
contig_5   614     0.329   0  163.557  Nematoda        2000.0      0
contig_6   216     0.1944  0  25.88    Tardigrada      4000.0      2
contig_7   4060    0.2584  0  52.312   Nematoda        2000.0      0
contig_8   2346    0.2801  0  91.742   unresolved      2000.0      1
contig_9   1599    0.2439  0  74.757   Nematoda        200.0       0
contig_10  6273    0.3067  0  310.634  no-hit          0.0         None

• The main header (##) contains version number, input files and parameters used while creating the blobDB file.
• The table header (#) indicates the names of the columns (explained in the table below).
• All following rows contain information about the sequences in the order they appear in the assembly file.

• If N > 1 coverage files are provided, N+1 coverage columns would show up in the table. One column per coverage files, and an additional column listing the sum of coverages across all files.
• The last three columns list information about the taxonomy at the taxonomic rank of "phylum" under the tax-rule "best-sum".
• If N > 1 taxonomic ranks are specified using the -r argument, additional columns will appear in the table.
• If the --hits flag is used, the table will include the sum of scores by hits file for each taxID
• The headers of the "taxonomy" columns are numbered (1-based) to ease filtering using command line applications such as GNU awk or UNIX/LINUX cut.

3. Create a blobplot

./blobtools plot \
 -i example/blobDB.json \
 -o example/

• This generates three files:
• the blobplot blobDB.json.bestsum.phylum.p7.span.100.blobplot.bam0.png
• the readcovplot blobDB.json.bestsum.phylum.p7.span.100.blobplot.read_cov.bam0.png
• the stats file blobDB.json.bestsum.phylum.p7.span.100.blobplot.stats.txt