mirdeep2
fastp
| mirdeep2 | fastp | |
|---|---|---|
| 1 | 9 | |
| 129 | 1,785 | |
| 0.0% | 2.9% | |
| 2.5 | 4.7 | |
| 6 months ago | about 1 month ago | |
| Perl | C++ | |
| GNU General Public License v3.0 only | MIT License |
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mirdeep2
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miRDeep2_core_algorithm.pl error
https://easyupload.io/hxygao
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?
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
galaxy - Data intensive science for everyone.
OTTO - Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
readfq - A simple tool to calculate reads number and total base count in FASTQ file
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
glslSmartDeNoise - Fast glsl deNoise spatial filter, with circular gaussian kernel, full configurable
miRPV - An Automated pipeline for miRNA identification and validation
nextclade - Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
alevin-fry - 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
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