Heng Li

Minimap2: pairwise alignment for nucleotide sequences

Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic cont...

Twelve years of SAMtools and BCFtools

Abstract Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion an...

Inference of human population history from individual whole-genome sequences

Fast and accurate short read alignment with Burrows–Wheeler transform

Abstract Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A...

The Sequence Alignment/Map format and SAMtools

Abstract Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads ...

Fast and accurate long-read alignment with Burrows–Wheeler transform

Abstract Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short r...

Tabix: fast retrieval of sequence features from generic TAB-delimited files

Abstract Summary: Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves fe...