Comments (2)
alexeigurevich
commented on July 23, 2024
The initial idea is to show contigs which are connected to each other according to GFA file. These connections may be shown pretty much the way we do for presenting misassembled blocks related to the same contig: special section in Contig info window and grey arrows on Alignment overview pane.
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sjackman
commented on July 23, 2024
Read the genome assembly contig overlap graph in Graphical Fragment Assembly (GFA) format and display the mean read coverage of the contig and links to the adjacent overlapping contigs. GFA is an emerging standard for genome assembly graphs originally proposed by Heng Li and now maintained by a community including myself. It is implemented by a number of assemblers and tools, including the visualization tool Bandage, which I also use for assessing genome assembly correctness. Icarus and Bandage complement each other nicely. See https://github.com/pmelsted/GFA-spec
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Related Issues (20)
- Feature quest: TSV output for relocations, transslocations, etc
- There is a huge difference between the results in the summary and the combined_reference.
- Error while creating Krona plots HOT 1
- ERROR! File not found (contigs) running on biocontainers/quast:5.2.0 HOT 4
- MetaQUAST 5.2.0 reference genome "not in list" error when "Summarizing results..."
- metaquast coloring error for > 14 samples
- OSError: [Errno 22]
- Error creating Krona plots in metaquast.py HOT 8
- Version of installed minimap2 differs from its version in the QUAST package (2.24) HOT 1
- Augustus busco not running with a conda install
- ERROR! Skipping S7KLEB_S14_L001_R2_001.fastq.00.0_0.cor.fastq.gz because it contains non-ACGTN characters. HOT 1
- [Errno 30] Read-only file system: '/usr/local/lib/python3.10/dist-packages/quast_libs/bwa/make.log' HOT 2
- Issues with the installation
- Issues about 'quast-download-busco' HOT 2
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- No space left on device HOT 5
- Bam files in output HOT 1
- What size of genome fraction can be considered low？
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