Top all-time · #6730
Heng Li
Personal blog · lh3.github.ioscienceprogramming
Heng Li's personal blog at lh3.github.io covers science and programming. Since 2015, 12 different Hacker News readers have linked it 16 times, most often “Fast high-level programming languages”. It is still writing: the last post was on 2026-10-31, and you can follow it by feed.
Too few sampled comments (10) to say how often HN recommends it.?
Why HN links it
HN readers link Heng Li's blog for posts on programming language speed in bioinformatics, comparing Nim, Crystal, Julia, Go and PyPy, plus DNA file compression and quality-score binning.
Summarised by Claude from a sample of 10 HN comments that link here. Each comment is marked recommending, critical or neutral (citing without judging); how this works.
Most-linked posts?
- Fast high-level programming languages4 people · 4 mentions · first linked 2020-05-18
- The AI Rewrite Dilemma2 people · 2 mentions · first linked 2026-04-17
What Hacker News says?
Agreed on usefulness of random access. Here's a couple more links on seekable gzip compression: http://lh3.github.io/2014/07/05/random-access-to-zlib-compre... http://www.ebaytechblog.com/2015/10/09/gzinga-seekable-and-s...
Comment linking /2014/07/05/random-access-to-zlib-compressed-files/
on “Stop using gzip”Submitted Fast high-level programming languages as a story · 124 points
HN discussionrelated: Biofast benchmark ( Nim, Julia, Go, Pypy, C, Crystal, .. ) "Benchmarking programming languages/implementations for common tasks in Bioinformatics" https://github.com/lh3/biofast#fqcnt https://lh3.github.io/2020/05/17/fast-high-level-programming... HN: https://news.ycombinator.com/item?id=23229657
Comment linking /2020/05/17/fast-high-level-programming-languages
on “Why I Use Nim instead of Python for Data Processing”Submitted What high-performance language to learn [for bioinformatics]? as a story · 5 points
HN discussionThis is a good write up imo: http://lh3.github.io/2020/05/17/fast-high-level-programming-...
Comment linking /2020/05/17/fast-high-level-programming-languages
on “NimConf 2020 Videos”Submitted Author of genome industry's BAM file format discusses the MPEG-G format as a story · 3 points
HN discussionCompletely anecdotal: - In my small benchmarks, Crystal is very fast - In benchmarks not my own, Crystal is very fast - Crystal has a very nice batteries included stdlib. Benchmarks that aren't mine: http://lh3.github.io/2020/05/17/fast-high-level-programming-... The only other language that is high level in its ballpark is D.
Comment linking /2020/05/17/fast-high-level-programming-languages
on “Go vs. Crystal Performance”Submitted The AI Rewrite Dilemma as a story · 2 points
HN discussionThe idea is far older than BWA. The entire point of the Burrows-Wheeler transform is to create a compact order-k "language model" for every value of k simultaneously. And then use that for data compression. David Wheeler reportedly had the idea in the early 80s, but he rejected it as impractical. Then he tried publishing it with Michael Burrows in the early 90s, but it was rejected from the Data Compression Conferen…
Comment linking /2024/04/12/where-did-bwa-come-from
on “Infini-Gram: Scaling unbounded n-gram language models to a trillion tokens”Submitted Random access to zlib compressed files as a story · 2 points
HN discussionSee https://lh3.github.io/2020/05/17/fast-high-level-programming... Also I should note that Julia performance greatly improved since. Next week there should be the 1.6.0 release, which will have even better numbers.
Comment linking /2020/05/17/fast-high-level-programming-languages
on “PyPy 7.3.2 triple release: Python 2.7, 3.6, and 3.7”Submitted On Maintaining Bioinformatics Software as a story · 1 points
HN discussionThere are many people working on various aspects of DNA graphs - for example, there's now the FASTG format, a replacement for the FASTA format which is essentially a graph in text form: http://fastg.sourceforge.net/ Some assemblers (SPAdes?) have started to support this format, but most downstream software only uses the FASTA format (the non-graph version from a single genome/representation). Heng Li (somewhat now t…
Comment linking /2014/07/25/on-the-graphical-representation-of-sequences/
on “As DNA reveals its secrets, scientists are assembling a new picture of humanity”I'm not sure why gzip still pops up for FASTQ data, as it is quite easy to bin the quality scores, align it against a reference genome and compress it as e.g. CRAM [1]. With 8 bins, the variant calling accuraccy seems to be preserved, while drastically reducing the file size. [1]: https://lh3.github.io/2020/05/25/format-quality-binning-and-...
Comment linking /2020/05/25/format-quality-binning-and-file-sizes
on “We're wasting money by only supporting gzip for raw DNA files”See Heng's tweet about the post: https://twitter.com/lh3lh3/status/1765822352661618836 ... and also his previous post comparing a couple of fast languages, including Rust, C, Crystal, Nim, Julia, Go and PyPy: Post: https://lh3.github.io/2020/05/17/fast-high-level-programming... HN: https://news.ycombinator.com/item?id=23229657
Comment linking /2020/05/17/fast-high-level-programming-languages
on “What high-performance language to learn [for bioinformatics]?”There has been a bit of a 'trend' to rewrite common bioinformatics/comp-bio into faster languages (Rust) via LLMs, OP's repo seems to be an early example. Seqera Labs has a bit of a manifesto: https://rewrites.bio/ Heng Li has an overview here too: https://lh3.github.io/2026/04/17/the-ai-rewrite-dilemma IMHO it's... OK? Bioinformatics code quality is generally poor, untrained biologists writing functioning code that…
Comment linking /2026/04/17/the-ai-rewrite-dilemma
on “Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop”
