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My Homepage at SourceForge.net, GitHub, Twitter, Disqus, publications at ResearcherID, Google Scholar and FTP at Broad Institute.
Posts 
- 28 Sep 2024 » Why is bwa-aln used for ancient DNA reads?
- 12 Apr 2024 » Where did BWA come from?
- 29 Mar 2024 » On the definition of pangenome
- 05 Mar 2024 » What high-performance language to learn?
- 21 Oct 2022 » Random open syncmers
- 28 Sep 2022 » A few suggestions for creating command line interfaces
- 10 Oct 2021 » Introducing dual assembly
- 06 Jul 2021 » Remapping an aligned BAM
- 04 Jul 2021 » Designing a command-line interface
- 17 May 2021 » An FM-index of 400k SARS-CoV-2 genomes
- 17 Apr 2021 » Concepts in phased assemblies
- 15 Mar 2021 » SNP vs SNV
- 11 Jan 2021 » Minigraph as a multi-assembly SV caller
- 25 Dec 2020 » Evaluating collapsed misassembly with asmgene
- 27 May 2020 » Base quality scores are essential to short read variant calling
- 25 May 2020 » Format, quality binning and file size
- 17 May 2020 » Fast high-level programming languages
- 08 Apr 2020 » auN: a new metric to measure assembly contiguity
- 12 Jul 2019 » On a reference pan-genome model (Part II)
- 08 Jul 2019 » On a reference pan-genome model
- 18 May 2019 » How much does developement time matter?
- 11 Mar 2019 » On maintaining bioinformatics software
- 21 Dec 2018 » SAM/BAM/samtools is 10 years old
- 25 Nov 2018 » On the definition of sequence identity
- 12 Nov 2018 » Seqtk: code walkthrough
- 28 Sep 2018 » On the MPEG-G alignment format
- 02 Apr 2018 » Minimap2 and the future of BWA
- 27 Mar 2018 » The history the MD tag and the CIGAR X operator
- 15 Nov 2017 » Immature thoughts on assembly De Bruijn graphs
- 13 Nov 2017 » Which human reference genome to use?
- 24 Jul 2017 » On NovaSeq Base Quality
- 07 Dec 2015 » Bioconda: a capable bio-software package manager
- 05 Oct 2015 » A reimplementation of symmetric DUST
- 30 Jul 2015 » A few comments on GraphMap
- 24 Jun 2015 » My thoughts on sharing genotype and phenotype data
- 25 Apr 2015 » A few hours with docker
- 23 Feb 2015 » The unary representation of variants
- 23 Feb 2015 » The problems with the VCF model
- 13 Feb 2015 » Correcting Illumina sequencing errors: extended background
- 27 Jan 2015 » The early history of the SAM/BAM format
- 10 Dec 2014 » BWA-MEM for long error-prone reads
- 03 Nov 2014 » On HiSeq X10 Base Quality
- 25 Jul 2014 » On the graphical representation of sequences
- 23 Jul 2014 » First update on GFA
- 20 Jul 2014 » Alternatives to PSMC
- 19 Jul 2014 » A proposal of the Grapical Fragment Assembly format
- 13 Jul 2014 » On the trend of disk-based algorithms
- 12 Jul 2014 » About static linking
- 07 Jul 2014 » Abreak: evaluating de novo assemblies
- 05 Jul 2014 » Random access to zlib compressed files
- 05 Jul 2014 » My blog