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.
- Assembly files generated by certain genome assembly programs contain coverage information in the header lines.
createis able to parse this information if the assembly type is specified using the
- However, this only includes base-coverage and hence does not allow plotting readcovplots.
- The output of the following assemblers is supported:
- COV files are a custom file-format written by BlobTools
create(after parsing a mapping file, a COV file is written automatically for future use)
- they contain all the information needed for BlobTools
- 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
Updated over 6 years ago