fastp
glslSmartDeNoise
| fastp | glslSmartDeNoise | |
|---|---|---|
| 9 | 1 | |
| 1,775 | 235 | |
| 2.3% | - | |
| 4.7 | 0.0 | |
| 27 days ago | over 2 years ago | |
| C++ | C++ | |
| MIT License | BSD 2-clause "Simplified" License |
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fastp
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R pipelines for bulk RNA-seq analyses
fastp + multiQC + Salmon + DESeq2 all some nextflow workflow. It is a good exercise (not complicated) to create the pipeline from scratch the first time to properly understand each tool.
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NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
1) QC the data with fastp. This'll trim out adapters and toss reads that are poor quality.
- Illumina adapters and quality trimming
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Low-complexity sequence filtering tool
fastp has an adjustable low complexity filter option.
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Can you evaluate my pipeline?
- in terms of preprocessing and QC, I prefer fastp (https://github.com/OpenGene/fastp)
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Current QC tools for short read and long read sequencing
I generally use fastp as an all-in-one tool for short reads: https://github.com/OpenGene/fastp
- Qurstion about automating trimming process
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What methods (conda installable only please) can you use to determine the complexity of a fastq file? (e.g., kmer analysis)
I don't know if this fits exactly what you need, but I'm using fastp to check my fastq.gz files lately: https://github.com/OpenGene/fastp. You can install it via conda.
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A tool to count basepair in fastq file
If you also need some other basic statistics or want to filter the reads you can try fastp (https://github.com/OpenGene/fastp). If only the basepair count is needed, awk might be the fastest solution as suggested before.
glslSmartDeNoise
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Made some sort of GI in 2D. At least I can cook eggs on my laptop with it.
In the demo the denoise I used was actually very ineffective. I now use a combination of temporal denoise (which sounds more advanced than it is, it's literally just interpolating each pixel with the previous frame, which is super cheap but too much causes ghosting), and the denoise algorithm from here which is amazing: https://github.com/BrutPitt/glslSmartDeNoise
What are some alternatives?
galaxy - Data intensive science for everyone.
glslViewer - Console-based GLSL Sandbox for 2D/3D shaders
readfq - A simple tool to calculate reads number and total base count in FASTQ file
3d-game-shaders-for-beginners - 🎮 A step-by-step guide to implementing SSAO, depth of field, lighting, normal mapping, and more for your 3D game.
nextclade - Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
glslang - Khronos-reference front end for GLSL/ESSL, partial front end for HLSL, and a SPIR-V generator.
readfq - Fast multi-line FASTA/Q reader in several programming languages
seqtk - Toolkit for processing sequences in FASTA/Q formats
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
bowtie2 - A fast and sensitive gapped read aligner
Sniffles - Structural variation caller using third generation sequencing
kraken2 - The second version of the Kraken taxonomic sequence classification system