readfq
biofast
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readfq
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Training resources for Biopython?
Heng Li has a FASTQ/FASTA reader that I generally cut and paste into my code rather than use Biopython. Biopython has a very rich model for sequence data but you generally don't need 90% of it and it comes at a significant performance cost.
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Extract sequences given FASTA + list of starts and ends?
Just slap Heng Li's FASTQ/A parsing function in, load in your read, then loop through your coordinates and slice the sequence.
biofast
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Parsing huge files in Python
FYI: the python packages I mentioned earlier can all directly read gzip'd fastq files. See also this repo for examples.
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Does Rust Support Reading in FATSA files?
needletail is rated in the Heng Li benchmark (https://github.com/lh3/biofast/)
- Why I Use Nim instead of Python for Data Processing
What are some alternatives?
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
nimtorch - PyTorch - Python + Nim
bioawk - BWK awk modified for biological data
scikit-bio - scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
PrimesResult - The results of the Dave Plummer's Primes Drag Race
biomisc - collection of miscellaneous command line bioinformatic scripts
viroiddb - A curated database of all available viroid-like RNA sequences
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
RecursiveFactorization.jl
benchmarks - Some benchmarks of different languages
Primes - Prime Number Projects in C#/C++/Python