deML
fastp
deML | fastp | |
---|---|---|
1 | 9 | |
45 | 1,785 | |
- | 2.9% | |
10.0 | 4.7 | |
over 1 year ago | about 1 month ago | |
C++ | C++ | |
GNU General Public License v3.0 only | MIT License |
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.
deML
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Fastq splitting help
I'm not sure it's maintained anymore, and I don't know if it's compatible with whatever kind of barcode/index you have, but deML does demultiplexing more accurately and thoroughly than anyone seems to care about.
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?
galaxy - Data intensive science for everyone.
readfq - A simple tool to calculate reads number and total base count in FASTQ file
glslSmartDeNoise - Fast glsl deNoise spatial filter, with circular gaussian kernel, full configurable
nextclade - Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
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
CHM13 - The complete sequence of a human genome
TPMCalculator - TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files