biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB (by wheretrue)
cramino
A *fast* tool for BAM/CRAM quality evaluation, intended for long reads (by wdecoster)
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.
biobear
Posts with mentions or reviews of biobear.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-24.
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biobear -- python package with minimal dependencies for bioinformatic file parsing and querying using rust and polars as the backend
Last time I'll try, but again you aren't understanding things and with all due respect seem to be stuck in the past. It works fine on Windows w/o maturin, but you're so keen to say something w/o understanding you're missing important details... look again and then look where the other job failed... https://github.com/wheretrue/biobear/actions/runs/4791174939/jobs/8521250054... if you're having issues with it please file an issue on github.
cramino
Posts with mentions or reviews of cramino.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-24.
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biobear -- python package with minimal dependencies for bioinformatic file parsing and querying using rust and polars as the backend
What do you see as the use case for this, specifically as it relates to the BAM reading? I've used pysam to read and iterate bamfiles to generate custom summary reports but this can be very slow with large files with many records. I know there are some things written in rust that show significant speed improvements (for example a tool I used nanostat was partially rewritten as cramino and purports to be much faster).
What are some alternatives?
When comparing biobear and cramino you can also consider the following projects:
adam - ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.