fastp
fasql
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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.
fasql
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Training resources for Biopython?
Shameless self promotion, but my company released an open source library that reads fasta and fastq files in python or other languages... https://github.com/wheretrue/fasql -- obv biased, but it's faster than biopython and has a lower footprint when you just need that.
- Show r/bioinformatics: fasql, a way to run SQL queries on FASTA and FASTQ files
What are some alternatives?
galaxy - Data intensive science for everyone.
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
readfq - A simple tool to calculate reads number and total base count in FASTQ file
h3-duckdb - Bindings for H3 to DuckDB
glslSmartDeNoise - Fast glsl deNoise spatial filter, with circular gaussian kernel, full configurable
readfq - Fast multi-line FASTA/Q reader in several programming languages
nextclade - Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
seqtk - Toolkit for processing sequences in FASTA/Q formats
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