A FASTA-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
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Short reads usually refer to the initial pieces of sequencing data that you had before you assembled them into longer contigs. In other words, these are the kinds of reads you could get out of a technique like Sanger sequencing. Knowing how those short reads align to your contigs is vital for analysis (In fact, that’s a lot of the functionality of a profile-db!).
In anvi’o, you can currently get short reads from four sources:
- from a bam-file by running the program anvi-get-short-reads-from-bam
- from a gene in a contigs-db by running the program anvi-get-short-reads-mapping-to-a-gene
- from something (like a contig) within a fasta file by running the program anvi-script-get-short-reads-matching-something
- by generating mock short read data from assembled contigs (as done in the program anvi-script-gen-short-reads).
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