corpus.blog
56,966 blogs · [ { "id": "01a0879a-614b-702d-b005-f8834d74af73", "title": "Minibwa is the new bwa-mem", "url": "http://lh3.github.io/2026/07/04/minibwa-is-the-new-bwa", "published_at": "2026-07-04T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834dfea1bc", "title": "The AI Rewrite Dilemma", "url": "http://lh3.github.io/2026/04/17/the-ai-rewrite-dilemma", "published_at": "2026-04-17T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834e8e65e8", "title": "Our journey through low-complexity regions", "url": "http://lh3.github.io/2025/09/29/on-low-complexity-regions", "published_at": "2025-09-29T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834e9f4f72", "title": "A quick look at Roche's SBX", "url": "http://lh3.github.io/2025/09/11/a-quick-look-at-roches-sbx", "published_at": "2025-09-11T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834ec79fa4", "title": "Short RNA-seq read alignment with minimap2", "url": "http://lh3.github.io/2025/04/18/short-rna-seq-read-alignment-with-minimap2", "published_at": "2025-04-18T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834f0b4b83", "title": "Why is bwa-aln used for ancient DNA reads?", "url": "http://lh3.github.io/2024/09/28/why-is-bwa-aln-still-used", "published_at": "2024-09-28T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834f14a566", "title": "Where did BWA come from?", "url": "http://lh3.github.io/2024/04/12/where-did-bwa-come-from", "published_at": "2024-04-12T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834fd1df2d", "title": "On the definition of pangenome", "url": "http://lh3.github.io/2024/03/29/what-is-a-pangenome", "published_at": "2024-03-29T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834fe0ea58", "title": "What high-performance language to learn?", "url": "http://lh3.github.io/2024/03/05/what-high-performance-language-to-learn", "published_at": "2024-03-05T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8834fe6bf2d", "title": "Random open syncmers", "url": "http://lh3.github.io/2022/10/21/random-open-syncmers", "published_at": "2022-10-21T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88350028c6e", "title": "A few suggestions for creating command line interfaces", "url": "http://lh3.github.io/2022/09/28/additional-recommendations-for-creating-command-line-interfaces", "published_at": "2022-09-28T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88350844077", "title": "Introducing dual assembly", "url": "http://lh3.github.io/2021/10/10/introducing-dual-assembly", "published_at": "2021-10-10T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835142cdda", "title": "Remapping an aligned BAM", "url": "http://lh3.github.io/2021/07/06/remapping-an-aligned-bam", "published_at": "2021-07-06T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835196418c", "title": "Designing a command-line interface", "url": "http://lh3.github.io/2021/07/04/designing-command-line-interfaces", "published_at": "2021-07-04T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835286f81a", "title": "An FM-index of 400k SARS-CoV-2 genomes", "url": "http://lh3.github.io/2021/05/17/an-fm-index-of-400k-sars-cov-2-genomes", "published_at": "2021-05-17T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883533a8951", "title": "Concepts in phased assemblies", "url": "http://lh3.github.io/2021/04/17/concepts-in-phased-assemblies", "published_at": "2021-04-17T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88353b4f921", "title": "SNP vs SNV", "url": "http://lh3.github.io/2021/03/15/snp-vs-snv", "published_at": "2021-03-15T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835442f3e0", "title": "Minigraph as a multi-assembly SV caller", "url": "http://lh3.github.io/2021/01/11/minigraph-as-a-multi-assembly-sv-caller", "published_at": "2021-01-11T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88354b78929", "title": "Evaluating collapsed misassembly with asmgene", "url": "http://lh3.github.io/2020/12/25/evaluating-assembly-quality-with-asmgene", "published_at": "2020-12-25T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88355b2a870", "title": "Base quality scores are essential to short read variant calling", "url": "http://lh3.github.io/2020/05/27/base-quality-scores-are-essential-to-short-read-variant-calling", "published_at": "2020-05-27T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88355c56db6", "title": "Format, quality binning and file size", "url": "http://lh3.github.io/2020/05/25/format-quality-binning-and-file-sizes", "published_at": "2020-05-25T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835615a006", "title": "Fast high-level programming languages", "url": "http://lh3.github.io/2020/05/17/fast-high-level-programming-languages", "published_at": "2020-05-17T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88356fb8b9c", "title": "auN: a new metric to measure assembly contiguity", "url": "http://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity", "published_at": "2020-04-08T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883574cd9ad", "title": "On a reference pan-genome model (Part II)", "url": "http://lh3.github.io/2019/07/12/on-a-reference-pan-genome-model-part-ii", "published_at": "2019-07-12T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88357f67f63", "title": "On a reference pan-genome model", "url": "http://lh3.github.io/2019/07/08/on-a-reference-pan-genome-model", "published_at": "2019-07-08T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88358a6defe", "title": "How much does developement time matter?", "url": "http://lh3.github.io/2019/05/18/how-much-does-developer-time-matter", "published_at": "2019-05-18T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88358daa0d5", "title": "On maintaining bioinformatics software", "url": "http://lh3.github.io/2019/03/11/on-maintaining-bioinformatics-software", "published_at": "2019-03-11T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883592fcb49", "title": "SAM/BAM/samtools is 10 years old", "url": "http://lh3.github.io/2018/12/21/sambamsamtools-is-10-years-old", "published_at": "2018-12-21T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835987c22b", "title": "On the definition of sequence identity", "url": "http://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity", "published_at": "2018-11-25T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835a57fcde", "title": "Seqtk: code walkthrough", "url": "http://lh3.github.io/2018/11/12/seqtk-code-walkthrough", "published_at": "2018-11-12T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835b28d81c", "title": "On the MPEG-G alignment format", "url": "http://lh3.github.io/2018/09/28/on-the-mpeg-g-alignment-format", "published_at": "2018-09-28T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835c09291f", "title": "Minimap2 and the future of BWA", "url": "http://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa", "published_at": "2018-04-02T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835c521642", "title": "The history the MD tag and the CIGAR X operator", "url": "http://lh3.github.io/2018/03/27/the-history-the-cigar-x-operator-and-the-md-tag", "published_at": "2018-03-27T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835c541715", "title": "Immature thoughts on assembly De Bruijn graphs", "url": "http://lh3.github.io/2017/11/15/on-assembly-de-bruijn-graphs", "published_at": "2017-11-15T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835ccb182c", "title": "Which human reference genome to use?", "url": "http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use", "published_at": "2017-11-13T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835ce59546", "title": "On NovaSeq Base Quality", "url": "http://lh3.github.io/2017/07/24/on-nonvaseq-base-quality", "published_at": "2017-07-24T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835d8cd405", "title": "Bioconda: a capable bio-software package manager", "url": "http://lh3.github.io/2015/12/07/bioconda-the-best-package-manager-so-far", "published_at": "2015-12-07T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835dfe4f83", "title": "A reimplementation of symmetric DUST", "url": "http://lh3.github.io/2015/10/05/an-reimplementation-of-symmetric-dust", "published_at": "2015-10-05T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835e36f4f5", "title": "A few comments on GraphMap", "url": "http://lh3.github.io/2015/07/30/a-few-comments-on-graphmap", "published_at": "2015-07-30T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835ee12209", "title": "My thoughts on sharing genotype and phenotype data", "url": "http://lh3.github.io/2015/06/24/my-thoughts-on-sharing-genomic-data", "published_at": "2015-06-24T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835f3b9416", "title": "A few hours with docker", "url": "http://lh3.github.io/2015/04/25/a-few-hours-with-docker", "published_at": "2015-04-25T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835f78c66c", "title": "The unary representation of variants", "url": "http://lh3.github.io/2015/02/23/the-unary-representation-of-variants", "published_at": "2015-02-23T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8835fb75b5b", "title": "The problems with the VCF model", "url": "http://lh3.github.io/2015/02/23/the-problems-with-the-vcf-model", "published_at": "2015-02-23T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8836052b915", "title": "Correcting Illumina sequencing errors: extended background", "url": "http://lh3.github.io/2015/02/13/comments-on-illumina-error-correction", "published_at": "2015-02-13T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883610d9868", "title": "The early history of the SAM/BAM format", "url": "http://lh3.github.io/2015/01/27/the-early-history-of-the-sambam-format", "published_at": "2015-01-27T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88361ed012d", "title": "BWA-MEM for long error-prone reads", "url": "http://lh3.github.io/2014/12/10/bwa-mem-for-long-error-prone-reads", "published_at": "2014-12-10T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883626e05d7", "title": "On HiSeq X10 Base Quality", "url": "http://lh3.github.io/2014/11/03/on-hiseq-x10-base-quality", "published_at": "2014-11-03T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8836322f53e", "title": "On the graphical representation of sequences", "url": "http://lh3.github.io/2014/07/25/on-the-graphical-representation-of-sequences", "published_at": "2014-07-25T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8836368dba9", "title": "First update on GFA", "url": "http://lh3.github.io/2014/07/23/first-update-on-gfa", "published_at": "2014-07-23T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88363d8ac92", "title": "Alternatives to PSMC", "url": "http://lh3.github.io/2014/07/20/alternatives-to-psmc", "published_at": "2014-07-20T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883640681da", "title": "A proposal of the Grapical Fragment Assembly format", "url": "http://lh3.github.io/2014/07/19/a-proposal-of-the-grapical-fragment-assembly-format", "published_at": "2014-07-19T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88364e7babc", "title": "On the trend of disk-based algorithms", "url": "http://lh3.github.io/2014/07/13/on-the-trend-of-disk-based-algorithms", "published_at": "2014-07-13T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f88365238512", "title": "About static linking", "url": "http://lh3.github.io/2014/07/12/about-static-linking", "published_at": "2014-07-12T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f8836614421c", "title": "Abreak: evaluating de novo assemblies", "url": "http://lh3.github.io/2014/07/07/abreak-evaluating-de-novo-assemblies", "published_at": "2014-07-07T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883661e0db0", "title": "Random access to zlib compressed files", "url": "http://lh3.github.io/2014/07/05/random-access-to-zlib-compressed-files", "published_at": "2014-07-05T00:00:00+00:00" }, { "id": "01a0879a-614b-702d-b005-f883669671f9", "title": "My blog", "url": "http://lh3.github.io/2014/07/05/my-blog", "published_at": "2014-07-05T00:00:00+00:00" } ] posts Claim your blog
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lh3.github.io

2026

Minibwa is the new bwa-memoriginal ↗
4 Jul 2026
The AI Rewrite Dilemmaoriginal ↗
17 Apr 2026

2025

Our journey through low-complexity regionsoriginal ↗
29 Sept 2025
A quick look at Roche's SBXoriginal ↗
11 Sept 2025
Short RNA-seq read alignment with minimap2original ↗
18 Apr 2025

2024

Why is bwa-aln used for ancient DNA reads?original ↗
28 Sept 2024
Where did BWA come from?original ↗
12 Apr 2024
On the definition of pangenomeoriginal ↗
29 Mar 2024
What high-performance language to learn?original ↗
5 Mar 2024

2022

Random open syncmersoriginal ↗
21 Oct 2022
A few suggestions for creating command line interfacesoriginal ↗
28 Sept 2022

2021

Introducing dual assemblyoriginal ↗
10 Oct 2021
Remapping an aligned BAMoriginal ↗
6 Jul 2021
Designing a command-line interfaceoriginal ↗
4 Jul 2021
An FM-index of 400k SARS-CoV-2 genomesoriginal ↗
17 May 2021
Concepts in phased assembliesoriginal ↗
17 Apr 2021
SNP vs SNVoriginal ↗
15 Mar 2021
Minigraph as a multi-assembly SV calleroriginal ↗
11 Jan 2021

2020

Evaluating collapsed misassembly with asmgeneoriginal ↗
25 Dec 2020
Base quality scores are essential to short read variant callingoriginal ↗
27 May 2020
Format, quality binning and file sizeoriginal ↗
25 May 2020
Fast high-level programming languagesoriginal ↗
17 May 2020
auN: a new metric to measure assembly contiguityoriginal ↗
8 Apr 2020

2019

On a reference pan-genome model (Part II)original ↗
12 Jul 2019
On a reference pan-genome modeloriginal ↗
8 Jul 2019
How much does developement time matter?original ↗
18 May 2019
On maintaining bioinformatics softwareoriginal ↗
11 Mar 2019

2018

SAM/BAM/samtools is 10 years oldoriginal ↗
21 Dec 2018
On the definition of sequence identityoriginal ↗
25 Nov 2018
Seqtk: code walkthroughoriginal ↗
12 Nov 2018
On the MPEG-G alignment formatoriginal ↗
28 Sept 2018
Minimap2 and the future of BWAoriginal ↗
2 Apr 2018
The history the MD tag and the CIGAR X operatororiginal ↗
27 Mar 2018

2017

Immature thoughts on assembly De Bruijn graphsoriginal ↗
15 Nov 2017
Which human reference genome to use?original ↗
13 Nov 2017
On NovaSeq Base Qualityoriginal ↗
24 Jul 2017

2015

Bioconda: a capable bio-software package manageroriginal ↗
7 Dec 2015
A reimplementation of symmetric DUSToriginal ↗
5 Oct 2015
A few comments on GraphMaporiginal ↗
30 Jul 2015
My thoughts on sharing genotype and phenotype dataoriginal ↗
24 Jun 2015
A few hours with dockeroriginal ↗
25 Apr 2015
The unary representation of variantsoriginal ↗
23 Feb 2015
The problems with the VCF modeloriginal ↗
23 Feb 2015
Correcting Illumina sequencing errors: extended backgroundoriginal ↗
13 Feb 2015
The early history of the SAM/BAM formatoriginal ↗
27 Jan 2015

2014

BWA-MEM for long error-prone readsoriginal ↗
10 Dec 2014
On HiSeq X10 Base Qualityoriginal ↗
3 Nov 2014
On the graphical representation of sequencesoriginal ↗
25 Jul 2014
First update on GFAoriginal ↗
23 Jul 2014
Alternatives to PSMCoriginal ↗
20 Jul 2014
A proposal of the Grapical Fragment Assembly formatoriginal ↗
19 Jul 2014
On the trend of disk-based algorithmsoriginal ↗
13 Jul 2014
About static linkingoriginal ↗
12 Jul 2014
Abreak: evaluating de novo assembliesoriginal ↗
7 Jul 2014
Random access to zlib compressed filesoriginal ↗
5 Jul 2014
My blogoriginal ↗
5 Jul 2014