Archive
2024
April
- April 12, 2024 » Where did BWA come from?
March
- March 29, 2024 » On the definition of pangenome
- March 5, 2024 » What high-performance language to learn?
2022
October
- October 21, 2022 » Random open syncmers
September
- September 28, 2022 » A few suggestions for creating command line interfaces
2021
October
- October 10, 2021 » Introducing dual assembly
July
- July 6, 2021 » Remapping an aligned BAM
- July 4, 2021 » Designing a command-line interface
May
- May 17, 2021 » An FM-index of 400k SARS-CoV-2 genomes
April
- April 17, 2021 » Concepts in phased assemblies
March
- March 15, 2021 » SNP vs SNV
January
- January 11, 2021 » Minigraph as a multi-assembly SV caller
2020
December
- December 25, 2020 » Evaluating collapsed misassembly with asmgene
May
- May 27, 2020 » Base quality scores are essential to short read variant calling
- May 25, 2020 » Format, quality binning and file size
- May 17, 2020 » Fast high-level programming languages
April
- April 8, 2020 » auN: a new metric to measure assembly contiguity
2019
July
- July 12, 2019 » On a reference pan-genome model (Part II)
- July 8, 2019 » On a reference pan-genome model
May
- May 18, 2019 » How much does developement time matter?
March
- March 11, 2019 » On maintaining bioinformatics software
2018
December
- December 21, 2018 » SAM/BAM/samtools is 10 years old
November
- November 25, 2018 » On the definition of sequence identity
- November 12, 2018 » Seqtk: code walkthrough
September
- September 28, 2018 » On the MPEG-G alignment format
April
- April 2, 2018 » Minimap2 and the future of BWA
March
- March 27, 2018 » The history the MD tag and the CIGAR X operator
2017
November
- November 15, 2017 » Immature thoughts on assembly De Bruijn graphs
- November 13, 2017 » Which human reference genome to use?
July
- July 24, 2017 » On NovaSeq Base Quality
2015
December
- December 7, 2015 » Bioconda: a capable bio-software package manager
October
- October 5, 2015 » A reimplementation of symmetric DUST
July
- July 30, 2015 » A few comments on GraphMap
June
- June 24, 2015 » My thoughts on sharing genotype and phenotype data
April
- April 25, 2015 » A few hours with docker
February
- February 23, 2015 » The unary representation of variants
- February 23, 2015 » The problems with the VCF model
- February 13, 2015 » Correcting Illumina sequencing errors: extended background
January
- January 27, 2015 » The early history of the SAM/BAM format
2014
December
- December 10, 2014 » BWA-MEM for long error-prone reads
November
- November 3, 2014 » On HiSeq X10 Base Quality
July
- July 25, 2014 » On the graphical representation of sequences
- July 23, 2014 » First update on GFA
- July 20, 2014 » Alternatives to PSMC
- July 19, 2014 » A proposal of the Grapical Fragment Assembly format
- July 13, 2014 » On the trend of disk-based algorithms
- July 12, 2014 » About static linking
- July 7, 2014 » Abreak: evaluating de novo assemblies
- July 5, 2014 » Random access to zlib compressed files
- July 5, 2014 » My blog