minimap2
or-tools
| minimap2 | or-tools | |
|---|---|---|
| 5 | 57 | |
| 1,688 | 10,466 | |
| - | 0.9% | |
| 7.6 | 9.9 | |
| 10 days ago | 1 day ago | |
| C | C++ | |
| GNU General Public License v3.0 or later | Apache License 2.0 |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
minimap2
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Ask HN: Comment here about whatever you're passionate about at the moment
Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.
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BLAST 10,000 genes?
No experience with this maybe try minimap2(https://github.com/lh3/minimap2) if this doesn't work fall back on blast/blat
- Truncating genome fastas to just overlapping regions
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Alignment of long reads to plasmid and generation of consensus sequence.
You can try minimap2 to align your long reads to your expected plasmid
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Questions about WGS mapping
It sounds like the mapping wasn't very good, you might want to try minimap2 as it is a newer algorithm.
or-tools
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or-tools VS timefold-solver - a user suggested alternative
2 projects | 4 Jan 2024
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A* Tricks for Videogame Path Finding
Small NP-hard problems aren't actually that bad. You can usually formulate them as eg a integer programming problem or a SMT problem, and throw an off-the-shelf solver at them.
You only need to learn the solver once, and you can re-use it for all kinds of problems. (Assuming that your instances don't have to be solved with low latency. Eg only as part of your level generation process, or at most when loading a randomly generated level, but not every frame or so.)
https://developers.google.com/optimization has a decent collection of tools.
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Ask HN: Comment here about whatever you're passionate about at the moment
Just saw that it looks like an upcoming release of OR-Tools might include reified tables: https://github.com/google/or-tools/commit/94f3d9b46870e7ea04...
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[P] Advice needed for what tool/algorithm is appropriate
Google OR - Tried to represent a solution to be a 5 dimensional matrix with an hour granularity. Dimensions are stations, program, project manager, day and time. If matrix[station][program][project manager][day][time] = 1, then that set is assigned, otherwise not. The main issue encountered here is about time slots, as they are not necessarily on a per hour basis. We tried time slots to be in a 5-minute interval. However, constructing the constraints that would adhere to each programs duration was proven to be difficult.
- What software is used in the field these days?
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Sudoku solver
If you are just interested in getting a solution or for having a reference solver: There is a sudoku example in the OR-Tools package that uses constraint programming.
- Matrix / 2d Array Puzzle-Like Problem
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Linear Programming
Not sql, but check out google’s OR-Tools. Hardly ever gets mentioned but looks very capable for some applications. https://developers.google.com/optimization
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Would anyone know how to auto schedule tasks based on certain constraints?
Then there's also the Google's solution: https://developers.google.com/optimization/
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Assignment to at most K groups from distance matrix?
start enumerating the properties you think the solution to your problem should have. once you have this, you should be able to reformulate those properties as constraints and then you can just plug this into a combinatorial solver such as https://developers.google.com/optimization
What are some alternatives?
bwa-mem2 - The next version of bwa-mem
OptaPlanner - Java Constraint Solver to solve vehicle routing, employee rostering, task assignment, maintenance scheduling, conference scheduling and other planning problems.
seqtk - Toolkit for processing sequences in FASTA/Q formats
optapy - OptaPy is an AI constraint solver for Python to optimize planning and scheduling problems.
seqstats - Quick summary statistics on fasta/fastq(.gz) files
pyomo - An object-oriented algebraic modeling language in Python for structured optimization problems.
slivar - genetic variant expressions, annotation, and filtering for great good.
SciPy - SciPy library main repository
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
optaplanner-quickstarts - Mirror of https://github.com/apache/incubator-kie-optaplanner-quickstarts
bwa-mem2 - The next version of bwa-mem
SWIG - SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.