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Hello,
I'm using seq_io to do some sliding window analysis of a 4Mb genome, but the size of the sequence remains limited. How should I configure my Rust program for the seqeunce size to be about 4M…
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Hi,
I am trying to execute Cactus on a set of custom newick+genome files (assembled similar to the example).
I am working on an HPC cluster with PBS PRO and not SLURM is there any way to execute the…
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Hi,
Thank you for developing a useful tool to merge SVs from sequencing datasets.
Currently, I am using HiFi data to call SVs using different callers: sniffles, cuteSV, pbsv, and svim for the Hi…
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Instead of doing global alignment on whole genome sequences, align just the searched subtype ORF sequence to the full query sequence.
The searched subtype ORF sequence should be prefixed and suffix…
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Hi ya'll!
I used Progressive Cactus to align whole genomes of 8 species. Then, using cactus-hal2maf with the --bedRanges option I was able to output an alignment including only genes of interest. W…
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Hi people,
I hope this is the right place to ask my question. If not, than please let me know an alternative. :)
I am kind of new in the world of whole genome alignments. I wanted to create a s…
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Is there a way to increase the visibility of SNPs at wider views? In the example below, I can see SNP differences between alignments in a 56 kb window, but not in a 140 kb window, which encompasses th…
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Hi Winnowmap Team,
I am trying to use winnowmap to do whole-genome alignments. In some cases, winnowmap is resulting in large unaligned regions like below:
![image](https://user-images.githubuserc…
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From igv-help group...
Hi,
We are trying to visualize bams generated by minimap2, run as part of the dipcall pipeline (https://github.com/lh3/dipcall), for the Genome in a Bottle HG002 Q100 T2T a…
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Dear AnchorWave team,
I am currently working on a project that involves calculating identities of 1M window size pairwise alignments in whole genome comparisons. I understand that AnchorWave is des…