Software

Below is a complete list of software written directly by lab members or supervised by our lab.

Amplicon sequence variants (ASVs) from modern long-read amplicon sequencing.

De novo long-read metagenome assembler, even for noisy sequences.

Long-read haplotypes for highly heterogeneous sequencing mixtures.

Fast approximate coverage for metagenomic binning.

Rapid taxonomic profiling for metagenomic samples through principled k-mer statistics.

Microbial strain phasing by flow-based MEC haplotyping.

Fast and robust average nucleotide identity by sparse approximate seed chaining.

Strain-level read reassignment.

Written by Andrew Zheng.

Fast polyploid haplotype phasing for long-read data.

Hybrid metagenomic assembler for long and short reads.

Contributions by Jim during his first internship in computational genomics.