readfq
Fast multi-line FASTA/Q reader in several programming languages (by lh3)
biomisc
collection of miscellaneous command line bioinformatic scripts (by olgatsiouri1996)
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.
-
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.
-
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.
biomisc
Posts with mentions or reviews of biomisc.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-04-06.
-
Biopython quarry on protein sequencing
if you know witch exactly residues do you want to retrieve from your pdb you can use this: subset_pdb_to_fasta.py
-
Extract sequences given FASTA + list of starts and ends?
i have made one with python: trim_fasta_by_coords.py. I have a newer version that deals with strands but since you work with proteins you don't need it
What are some alternatives?
When comparing readfq and biomisc you can also consider the following projects:
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
DnaChisel - :pencil2: A versatile DNA sequence optimizer
biofast - Benchmarking programming languages/implementations for common tasks in Bioinformatics
PDBaser - Protein preparation for MD, made faster and easier !
bioawk - BWK awk modified for biological data
pyfaidx - Efficient pythonic random access to fasta subsequences
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
pycm - Multi-class confusion matrix library in Python
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences