Mapping
Mapping is often used as an alternative way of reconstructing a genome from sequencing raw data, instead of trying to re-assemble it from scratch. Sparrowhawk offers this service through ska.rust (paper): a toolkit for prokaryotic (and other haploid and small genome beings) sequence analysis with split kmers.
General considerations
After processing, the mapped sequences are displayed in an interactive MSEABOARD sequence viewer directly in the browser.
Parameters
The values in brackets are the default ones:
- k [31]: controls the size of subsequences used in the algorithm. It is an odd integer that should be between ~17 up until 63.
- Proportion of reads [1.0]: a real number between 0 and 1 that allows you to choose, when you upload reads, what fraction of those you want to sample (if you want to do so).
- Min Illumina read quality [20]: integer 0–33; filters nucleotides below this quality score.
- Quality filter type [All bases]: dropdown; “No filter” / “Middle base” (only the central split-kmer base) / “All bases” (any base in the k-mer).
- Use canonical k-mers [false]: accounts for both strand orientations; recommended when using raw reads. Can only be set before uploading any file.
- Mask ambiguous bases [false]: replaces ambiguous bases in the output with
N. Can only be set before uploading any file. - Mask repeats [false]: masks repeated regions in the output with
N. Can only be set before uploading any file.
Example
The following data can be used to try out the mapper:
- Species: Mycobacterium tuberculosis
- Reference genome: GCA_000195955.2 (FASTA, gzipped)
- Reads to map (SRR30941327): forward and reverse