Fig. 3: Diagram of bioinformatic tools: gfa_parser and switch_error_screen. | Heredity

Fig. 3: Diagram of bioinformatic tools: gfa_parser and switch_error_screen.

From: Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes

Fig. 3

A Graphical representation of gfa_parser, which outputs FASTA sequences for all possible paths through a defined section of a graphical fragment assembly (GFA) file that are (i) directed from 5’ to 3’ and (ii) acyclic, such that no assembly path loops through a unitig multiple times. B An illustration describing switch_error_screen, which calculates a switch error index value across a sliding window based on soft clipping on the 5’ and 3’ ends of realigned reads. Two haplotypes are represented by color (red vs. blue). Soft clipping is represented by diagonal white lines through aligned reads.

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