Software & Database
Maintained by me
Most software I developed is available at the my GitHub page.
Sequence alignment
- minimap2 maps short and long genomic reads and long RNA-seq reads to a large reference database. It also performs full-genome pairwise alignment and finds overlaps between long reads.
- BWA aligns short sequence reads to a reference genome. Minimap2 is recommended for long-read mapping.
De novo assembly
- miniasm is a very fast overlapped-based de novo assembler for noisy long reads.
- FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. It consists of the following components:
- fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size. Fermi-lite is largely a miniature of FermiKit.
Miscellaneous
- seqtk is a set of fast and lightweight tools for processing sequences in the FASTA or FASTQ format.
- bioawk is an extension to Brian Kernighan's original awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
- htsbox is a fork of samtools/htslib, adding a few missing functionalities.
- lianti is a set of tools for short reads sequenced from the LIANTI single-cell protocol. It is a fork of htsbox.
- adna is a set of tools to process ancient DNA reads, such as merging overlapping reads and barcode-aware duplicate marking. It is a fork of lianti.
- tabtk is a set of tools for CSV or TAB-delimited formats.
- BGT is a compact file format for efficiently storing and querying whole-genome genotypes of tens to hundreds of thousands of samples.
- dna-nn efficiently identifies alpha satellite and hsat2,3 microsatellite sequences based on a deep learning model.
Maintained by others
- SAMtools/htslib is a suite of programs for interacting with high-throughput sequencing data. I created this project. It is now maintained by a team at the Sanger Institute.
Discontinued
- MAQ is a first-generation short-read mapper, now replaced by BWA.
- TreeSoft provides several softwares for reconstructing or manipulating phylogenetic trees. Some of its components are still used by Ensembl-Compara.
- TreeFam is a database of phylogenetic trees of animal genes. I am a key founder of this database. It is not maintained any more.
- TraceUtils is a program that calls heterozygotes from capillary sequencing trace files.
Contributed
- wtdbg2 is a novel de novo assembler for long noisy reads.