galaxy
fastp
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| galaxy | fastp | |
|---|---|---|
| 4 | 9 | |
| 1,313 | 1,768 | |
| 2.6% | 3.7% | |
| 10.0 | 4.7 | |
| 5 days ago | 22 days ago | |
| Python | C++ | |
| GNU General Public License v3.0 or later | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
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.
galaxy
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Need for GUIs for bioinformatic tools?
Maybe it would help you to look at the galaxy project: GitHub main site
- BIOINFORMATICS PROJECT
- Any bioinfo open source projects looking for contributors?
- Developed a new kind of dual extruder system on fully custom built 3D printer
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?
nextflow - A DSL for data-driven computational pipelines
readfq - A simple tool to calculate reads number and total base count in FASTQ file
Biopython - Official git repository for Biopython (originally converted from CVS)
glslSmartDeNoise - Fast glsl deNoise spatial filter, with circular gaussian kernel, full configurable
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
nextclade - Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
readfq - Fast multi-line FASTA/Q reader in several programming languages
galaxy_ng - Ansible Galaxy Server - Issues on https://forum.ansible.com Docs on https://galaxy-ng.readthedocs.io/
seqtk - Toolkit for processing sequences in FASTA/Q formats
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files