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godotgildor / fastq_compression_comparison

Creating a simple Docker image to help perform comparisons for FASTQ compression
MIT License
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Additional tools to evaluate #2

Open godotgildor opened 4 years ago

godotgildor commented 4 years ago

Clumpify: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/clumpify-guide/ MZPAQ: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547476/ GTZ: https://www.ncbi.nlm.nih.gov/pubmed/29297296 bsc: https://github.com/IlyaGrebnov/libbsc HARC: https://academic.oup.com/bioinformatics/article/34/4/558/4386919

godotgildor commented 4 years ago

Genie (MPEG-G compliant): https://sc19.supercomputing.org/proceedings/tech_poster/poster_files/rpost161s2-file2.pdf https://github.com/mitogen/genie

godotgildor commented 4 years ago

Also commercial solutions like Petagene: https://www.petagene.com/

KirillKryukov commented 3 years ago

Here are some more FASTQ compressors you can try.

Free: DSRC: https://github.com/refresh-bio/DSRC fastqz: https://github.com/fwip/fastqz FQSqueezer: https://github.com/refresh-bio/fqsqueezer Leon: https://github.com/GATB/leon LFastqC: https://github.uconn.edu/sya12005/LFastqC LFQC: https://github.com/mariusmni/lfqc Minicom: https://github.com/yuansliu/minicom NAF: https://github.com/KirillKryukov/naf Quip: https://github.com/dcjones/quip

Commercial: ALAPY: http://alapy.com/services/alapy-compressor/

Also see previous FASTQ and FASTA compressor benchmarks: https://doi.org/10.1038/nmeth.4037 https://doi.org/10.1093/gigascience/giaa072

divonlan commented 1 year ago

Also Genozip: www.genozip.com (commercial, free for academic use)

Huanle commented 1 year ago

would be nice if you can do some comparisons with bam compression tools ;-)

corneliusroemer commented 1 year ago

Add zstd, should be faster than gz for equal compression ratios.