bowtie2
seq
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bowtie2 | seq | |
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2 | 15 | |
615 | 634 | |
- | - | |
7.6 | 0.7 | |
about 2 months ago | over 1 year ago | |
C++ | C++ | |
GNU General Public License v3.0 only | Apache License 2.0 |
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
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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
seq
- Bioinformatics programming language
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A Python-based programming language for high-performance computational genomics
> Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications
- Seq – A programming language for computational genomics and bioinformatics
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Hacker News top posts: Sep 15, 2021
Seq: A programming language for high-performance computational genomics\ (17 comments)
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Seq: A programming language for high-performance computational genomics
They support both, and will deprecate Python 2 style soon.
What are some alternatives?
STAR - RNA-seq aligner
Nim - Nim is a statically typed compiled systems programming language. It combines successful concepts from mature languages like Python, Ada and Modula. Its design focuses on efficiency, expressiveness, and elegance (in that order of priority).
bwa-mem2 - The next version of bwa-mem
adam - ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
wyng-backup - Fast Time Machine-like backups for logical volumes & disk images
kraken2 - The second version of the Kraken taxonomic sequence classification system
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Biopython - Official git repository for Biopython (originally converted from CVS)
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites
bioconda-recipes - Conda recipes for the bioconda channel.