abPOA
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yangao07
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
Hello, I'm experimenting with adding abPOA as an option within [cactus](https://github.com/ComparativeGenomicsToolkit/cactus) ([manuscript](https://www.biorxiv.org/content/10.1101/730531v1)). Thanks for making a great tool -- it's amazingly fast. I was wondering if there's a way to...
I'm aligning a short sequence to a very long one, and they look like ``` ATATA ATATATATATAA ``` When I align them with abpoa, it puts the gap in the...
Hi @yangao07 , I've been experimenting a little with the seeding in abpoa and am wondering if it would be possible to add an option for users to provide alignment...
Hi Ya~~o~~n, I've expanded few sequences with flanking nucleotides, then I've aligned them, obtaining the MSA and consensus sequence. However, after aligning the expanded sequences, I would like to first...
Hello, I am trying to use abpoa as a dependency for one of my projects (https://github.com/HopedWall/rs-vgaligner), where I need to align a (sub)graph against some query sequences. In my project...
Hi all, first of all: great library! I was playing around with diploid mode and I ran into strange segmentation faults (when freeing `cons_cov`). From what I could see, in...
I have been getting some rare segmentation faults from abpoa. They only reproduce when compiling with sse4.1. I've been using sse4.1 to increase portability as well as save on cloud...
GFA output
Have you considered adding GFA output to abPOA? I am likely to make a patch to do this, but I wouldn't mind if you beat me to it. 🙂
Hello, Thank you very much for abPOA, it is a nice tool, installation was fast and easy. I would like to be able to incrementally update the POA graph. That...
I finally found a small reproducible example of an alignment problem. To reproduce on this input FASTA, [fail_smoothxg_block_3055.fa.txt](https://github.com/yangao07/abPOA/files/5334048/fail_smoothxg_block_3055.fa.txt): ``` abpoa -s -r 3 fail_smoothxg_block_3055.fa [simd_abpoa_align_sequence_to_subgraph1] Error in cg_backtrack. (4) ```