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# To Do
- [x] Literature review of spliced short read alignment methods (is anyone using Minimap2?)
- [x] Review Rust libraries for alignment and minimizers
- [x] Make stand-alone command line Ru…
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It would be useful if there was a function that automatically did pairwise alignment for all sequences in a list creating a new data structure that contained:
(1) an identity matrix (or distance)
(2)…
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Dot plot is a great way to visualise local sequence similarity. There are several tools to generate dot-plot, but it might be worth writing something simple of our own using pairwise alignment generat…
yeban updated
8 years ago
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Hi!
I have a question regarding handling of sequences with different length.
I usually align sequences with a fixed identity cutoff of 97% and, depending on the sample, different read length. `v…
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Hi,
does the version of Multiz in this repository works for aligning more than two species to a reference?
Thanks
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we want to collapse bubbles with size k since those will just be single-base mismatch
What lines in `dbga` are most pertinent to this?
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Hello everyone,
I have been working on a library with many different edit distance routines that use SIMD when possible to boost the speed of calculating edit distances on both long and short strin…
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As a novice user of PASTE2, I'm truly grateful for the provision of such a robust 3D spatial transcriptome reconstruction tool. Having successfully replicated results using the demo data, I'm now conf…
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Hello, I am trying to run some 3D scans using auto3DGM but I keep getting the following error. Error: 'rBind' is defunct.
Since R version 3.2.0, base's rbind() should work fine with S4 objects. Do y…
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Hi there,
I've been finding it quite hard to understand how to use the tool with a custom .fasta file. in my case I completely removed all the sequences from the sample_files and added my own (for…