Coverage file

Why is it needed?

A contains information regarding the base/read coverage of each sequence in an assembly file. Assuming an unbiased sequencing process, the base/read coverage reflects the molarity of the DNA molecule (represented by the sequence in the assembly) that went into the sequencing reaction.

The coverage information parsed by BlobTools is:

Base coverage

is used in the log-scaled y-axis in a blobplot
is used in both, log-scaled x-axis and y-axis in a covplot

Total number of reads and number of mapped reads
is used in the first two bars of a readcovplot
Read coverage
- is used in subsequent bars of a readcovplot

The details on how BlobTools parses coverage information are described in coverage parsing.

Mapping files

the following formats are supported:
BAM file
SAM file
CAS file

Assembly files

Assembly files generated by certain genome assembly programs contain coverage information in the header lines.
BlobTools create is able to parse this information if the assembly type is specified using the -y argument.
However, this only includes base-coverage and hence does not allow plotting readcovplots.
The output of the following assemblers is supported:
SPAdes
Velvet
Platanus

COV files

COV files are a custom file-format written by BlobTools map2cov and create (after parsing a mapping file, a COV file is written automatically for future use)
they contain all the information needed for BlobTools create.
their use is encouraged since parsing a COV file requires less time than parsing a mapping file.
an example of a COV file is shown below

## blobtools v1.0
## Total Reads = 15313
## Mapped Reads = 15313
## Unmapped Reads = 0
## Source(s) : example/mapping_1.bam
# contig_id	read_cov	base_cov
contig_1    369       90.406
contig_2    844       168.409
contig_3    188       43.761
contig_4    2096      456.313
contig_5    456       163.557
contig_6    52        25.88
contig_7    1005      52.312
contig_8    1008      91.742
contig_9    554       74.757
contig_10   8741      310.634