This GitHub organization keeps forks of repos developed by lab members since 2018. It lists past and present tools from the lab and serves as a backup. These forks are automatically synced with the parent repos and are not maintained here. If you want to create issues or send pull requests, please do so at the parent repos.
Selected tools maintained by current lab members:
- longcallD: small and large variant calling from genomic long reads
- ropebwt3: construction and utility of BWT for DNA string sets
- minisv: lightweight mosaic/somatic SV caller for long reads
- longcallR: SNP calling and haplotype-specific analysis from long RNA-seq reads
- Immuannot: annotating HLA and KIR genes in phased assemblies
- pangene: constructing a pangenome gene graph
- compleasm: a reimplementation of BUSCO for evaluating gene completeness
- hifieval: evaluating the accuracy of long-read error correction
- srf: assembler for satellite DNA
- miniprot: protein-to-genome alignment
- minigraph: pangenome construction and sequence-to-graph alignment
- minimap2: aligning long reads and contigs
Tools developed by past lab members:
- hifiasm: de novo assembler for accurate long reads
- ntsm: sample swap detection
- hifiasm-meta: metagenome assembler for accurate long reads
- T1K: HLA and KIR genotyper
- chromap: aligning short ChIP-seq, ATAC-seq or Hi-C reads
