community
An open community with an interest in developing and using new technologies for tensor data storage. (by zarr-developers)
tamtools
Create and manage hybrid reference assemblies to consolidate two original DNA alignments against different reference assemblies. (by tf318)
community | tamtools | |
---|---|---|
1 | 1 | |
19 | 3 | |
- | - | |
0.0 | 10.0 | |
6 months ago | almost 8 years ago | |
Python | ||
- | GNU General Public License v3.0 only |
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.
community
Posts with mentions or reviews of community.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-01-09.
-
We're wasting money by only supporting gzip for raw DNA files
The Zarr format is used in some genomics workflows (see https://github.com/zarr-developers/community/issues/19) and supports a wide range of modern compressors (e.g. Zstd, Zlib, BZ2, LZMA, ZFPY, Blosc, as well as many filters.)
tamtools
Posts with mentions or reviews of tamtools.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-01-09.
-
We're wasting money by only supporting gzip for raw DNA files
A few years ago I built some tools https://github.com/tf318/tamtools to store alignments against two different reference assemblies in an efficient way (taking advantage of the fact that the majority of each alignment to different assemblies would in fact be the same, just shifted in position).
The intent was to enhance this to store alignments against multiple references as new references are published, and probably to rewrite in Rust or C rather than the initial Python effort.
In retrospect I would be interested to know whether this domain-specific compression effort, with zstd to the resulting "hybrid" alignment, would be more efficient than just letting zstd do its own thing with a full set of individual alignments against the different references.
What are some alternatives?
When comparing community and tamtools you can also consider the following projects:
genozip - A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
zstd - Zstandard - Fast real-time compression algorithm
BEETL - BEETL