community
An open community with an interest in developing and using new technologies for tensor data storage. (by zarr-developers)
BEETL
BEETL (by BEETL)
community | BEETL | |
---|---|---|
1 | 1 | |
19 | 94 | |
- | - | |
0.0 | 1.2 | |
6 months ago | about 1 year ago | |
C++ | ||
- | BSD 2-clause "Simplified" License |
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.)
BEETL
Posts with mentions or reviews of BEETL.
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
If you have re-sequencing data of model species (which applies to >80% of generated sequencing data), the storage issue is often solved using CRAM/BAM formats. The FASTQ can be reconstructed if unmapped reads are stored in the file.
More general (pre-alignment) sequence compression methods never really took of (e.g. https://github.com/BEETL/BEETL). Probably because it helps so much to have common format that most workflows can start with. Here, the replacement of gzip with zstd would be a lower hanging fruit to start with.
What are some alternatives?
When comparing community and BEETL 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
tamtools - Create and manage hybrid reference assemblies to consolidate two original DNA alignments against different reference assemblies.
zstd - Zstandard - Fast real-time compression algorithm
Hail - Cloud-native genomic dataframes and batch computing