readfq
Fast multi-line FASTA/Q reader in several programming languages (by lh3)
fasql
DuckDB Extension for reading and writing FASTA and FASTQ Files (by wheretrue)
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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.
readfq
Posts with mentions or reviews of readfq.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-08.
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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.
fasql
Posts with mentions or reviews of fasql.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-08.
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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?
When comparing readfq and fasql you can also consider the following projects:
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
biofast - Benchmarking programming languages/implementations for common tasks in Bioinformatics
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bioawk - BWK awk modified for biological data
h3-duckdb - Bindings for H3 to DuckDB
biomisc - collection of miscellaneous command line bioinformatic scripts
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences