bowtie2
fastp
Our great sponsors
| bowtie2 | fastp | |
|---|---|---|
| 2 | 9 | |
| 618 | 1,768 | |
| - | 3.7% | |
| 7.6 | 4.7 | |
| 6 days ago | 21 days 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.
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.
bowtie2
-
NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).
- Computationally intensive steps in RNA-seq analysis
fastp
-
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.
-
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
-
Low-complexity sequence filtering tool
fastp has an adjustable low complexity filter option.
-
Can you evaluate my pipeline?
- in terms of preprocessing and QC, I prefer fastp (https://github.com/OpenGene/fastp)
-
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
-
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.
-
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?
STAR - RNA-seq aligner
galaxy - Data intensive science for everyone.
bwa-mem2 - The next version of bwa-mem
readfq - A simple tool to calculate reads number and total base count in FASTQ file
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
glslSmartDeNoise - Fast glsl deNoise spatial filter, with circular gaussian kernel, full configurable
seq - A high-performance, Pythonic language for bioinformatics
nextclade - Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites
readfq - Fast multi-line FASTA/Q reader in several programming languages
kraken2 - The second version of the Kraken taxonomic sequence classification system
seqtk - Toolkit for processing sequences in FASTA/Q formats