Heng Li's blog

Preprinted in 2013, bwa-mem is a popular mapper for 100+ bp short reads.

There have been multiple ongoing efforts (see Appendix below), and debates, regarding porting bioinformatics tools to Rust.

Those who inspect SVs often have probably noticed many SVs fall in low-complexity regions (LCRs) or tandem repeats and they are challenging to call.

Sequencing by Expansion (SBX) is Roche’s new short-read sequencing technology.

TL;DR: the new preset splice:sr in minimap2 can align short RNA-seq reads.

BWA implements three algorithms: bwa-aln, bwa-sw and bwa-mem.

My blog posts are often motivated by casual conversations with other scientists.

Historically, the term “pan-genome” (or more often “pangenome” in recent literature) was first coined by Sigaux in 2000 for a purpose distinct from current uses.

In the past couple of months, I have been asked several times about what language(s) to learn if someone wants to write high-performance programs.

A $k$-long sequence $P$ is a ($k$,$s$)-open-syncmer, $s\le k$, if $P[1,s]$ is the smallest among all $s$-mers in $P$.

Command-line interface, or CLI in brief, specifies how a user interacts with a program on the command line.

Definition.

This is a short post on how to remap short reads in an aligned BAM using bwa-mem.

This post is inspired by Vince’s tweet.

Leonardo Martins tweeted that xz can compress a 1.4 million SARS-CoV-2 genomes in a 39GB FASTA down to 74MB.

Concepts in phased assembly: Contig: a contiguous sequence in an assembly.

Ian Holmes has a twitter poll right now on the use of “SNP” (single-nucleotide polymorphism) versus “SNV” (single-nucleotide variant).

Honestly, I didn’t know what minigraph would be good for when I was writing the code.

Why?

In an earlier post a few days ago, I said “discarding base quality dramatically reduces variant calling accuracy”.

This short post evaluates the effect of format and quality binning on file sizes.

Background Python and R are slow when they can’t rely on functionality or libraries backed by C/C++.

Given a de novo assembly, we often measure the “average” contig length by N50.

I wrote a blog post on a potential reference pan-genome model.

In the last weekend, I made gfatools and minigraph open to the public.

I often hear developers saying “I do XYZ because it saves my time”.

In 2006, Ruiqiang Li, the now CEO of Novogene, said to me in Chinese: “you can’t maintain the TreeFam database forever”.

I wrote a commentary on the SAM/BAM format a while ago.

Sequence identity is a way to measure the similarity between two sequences.

On Twitter, Zach charlop-powers asked me to give a code walkthrough for seqtk.

SAM is a text format that is typically used to store the alignment of high-throughput sequence reads against a reference genome.

My minimap2 paper has been accepted for publication in Bioinformatics.

In the SAM format, the “X” and “=” CIGAR operators were not part of the original spec.

By mathematical definition, a k-order (or k-dimensional) De Bruijn graph, or ${\rm DBG}(k)$ in brief, over the DNA alphabet uses k-mers at vertices.

TL;DR: If you map reads to GRCh37 or hg19, use hs37-1kg: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz If you map to GRCh37 and believe decoy sequences help with better variant calling, use hs37d5: ftp://ftp-trac…

Introduction Illumina Inc. released NovaSeq earlier this year and provided sample data at BaseSpace several months later.

Getting Started Firstly, a few basic concepts.

I have just reimplemented the symmetric DUST algorithm (SDUST) for masking low-complexity regions.

GraphMap is a new long-read mapper initially tuned for error-prone ONT reads.

Today, Google and Broad Institute (my employer) have announced that they are teaming up to tackle genomic data.

Installing docker on Mac With all the buzz around docker, I finally decided to give it try.

This and the next posts were mostly written on the plane when I felt tired and did not have Internet connections.

As is discussed in my previous post, a major but potentially fixable problem with the VCF model is that we allow to and sometimes have to squeeze multiple alleles in one VCF line.

I enjoy writing 2-page Application Notes these days.

While I was looking for an ancient email on my old (first) macbook, I noticed the numerous email exchanges during the early days of the SAM/BAM format.

A recent paper published by Phil Ashton et al has triggered some discussions which subsequently moved to my domain: read mapping.

Illumina has recently released four lanes of NA12878 data from HiSeq X10.

Introduction Ever since the advent of the so-called Next-Generation Sequencing (NGS), we have been thinking about encoding all the population variations in a graph.

I was out of the town in the past few days, so have not been able to focus on GFA.

PSMC is my program to infer the historical effective population size from a diploid genome.