nextclade
fastp
| nextclade | fastp | |
|---|---|---|
| 2 | 9 | |
| 199 | 1,775 | |
| 2.5% | 2.3% | |
| 9.8 | 4.7 | |
| 9 days ago | about 1 month ago | |
| TypeScript | C++ | |
| MIT License | MIT License |
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nextclade
- Why does musl make my Rust code so slow? (2020)
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For SARS-CoV-2 genomic analysis, what is the difference in utility of a Pangolin Lineage versus a NextClade Clade (e.g. lineage B.1.617.2 vs clade 21A)?
Lineage and clade assignments--especially by Pangolin and Nextclade, respectively--seem to be the most popular way to characterize SARS-CoV-2 genomes and so I'm wondering how these two concepts are applied differently to inform our understanding of the pandemic.
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.
What are some alternatives?
pangolin - Software package for assigning SARS-CoV-2 genome sequences to global lineages.
galaxy - Data intensive science for everyone.
covid-19-api - A JavaScript library that provides a simple API for the Johns Hopkins University CSSE COVID-19 time series data.
readfq - A simple tool to calculate reads number and total base count in FASTQ file
BioExplorer - The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration
glslSmartDeNoise - Fast glsl deNoise spatial filter, with circular gaussian kernel, full configurable
covid19_scenarios - Models of COVID-19 outbreak trajectories and hospital demand
readfq - Fast multi-line FASTA/Q reader in several programming languages
iTeribus - Un'applicazione per la creazione e la compilazione automatica dei moduli di autodichiarazione COVID 19.
seqtk - Toolkit for processing sequences in FASTA/Q formats
k8s-folding-at-home - ⛑ Run folding@home on your Kubernetes cluster
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files