Genome vs Genome

[fergsc]

Hi,

Is VACmap set up to do genome vs genome alignments? I could run in -mode L, however an assembled genome would have much fewer errors.

thanks.

[micahvista]

Hi,

I will be releasing a new version of VACmap next week, which will include support for genome-to-genome alignments.

Currently, VACmap struggles with handling large sequences (over ~2 Mbps), as the frequent sequence splitting can cause excessive memory usage in some steps. These issues will be addressed in the upcoming version, and I will notify you once it's available.

Thank you for your patience!

Best regards, Hongyu Ding

[fergsc]

Great, I look forward to trying it.

[micahvista]

Hi,

VACmap now supports genome-to-genome alignments! Please use the following command:

vacmap -ref /ref.fasta -read /read.fasta -mode asm -t 8 -workdir /home/usr/workdir/ --H --fakecigar | samtools sort -@4 > alignments.sorted.bam samtools index -@4 alignments.sorted.bam

Make sure to provide a folder with the -workdir option for VACmap. It will check whether the folder exists; if not, VACmap will create it automatically.

The --H option uses hard clipping for clipped sequences in the CIGAR string, which helps reduce the output alignment file size. The --fakecigar option applies approximate CIGAR in the SA tag, also reducing file size (similar to minimap2).

Please note that genome-to-genome alignment can be memory-intensive. The more threads you use, the more memory is required, as VACmap will load more contigs into memory. The memory usage for VACmap in this mode is roughly equal to min(30 + threads, contig count in input file) GB.

While this genome-to-genome mode is newly developed and I have tested it with a few assemblies successfully, please feel free to contact me if you encounter any issues. I would greatly appreciate your feedback.

Thank you for your patience!

Best regards, Hongyu Ding