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Fastp Alternatives
Similar projects and alternatives to fastp
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rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
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WorkOS
The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
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nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
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KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
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NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better fastp alternative or higher similarity.
fastp reviews and mentions
Posts with mentions or reviews of fastp.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-12-09.
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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.
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Stats
Basic fastp repo stats
9
1,760
3.5
18 days ago
OpenGene/fastp is an open source project licensed under MIT License which is an OSI approved license.
The primary programming language of fastp is C++.
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