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a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
PanTax: Strain-level metagenomic profiling using pangenome graphs
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
Tool for plotting sequencing data along genomic coordinates.
A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
Get assembly statistics from FASTA and FASTQ files
a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
jq for binary formats - tool, language and decoders for working with binary and text formats
FastOMA is a scalable software package to infer orthology relationship.
A tool for generating consensus long-read assemblies for bacterial genomes
LexicMap: efficient sequence alignment against millions of prokaryotic genomes
Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
Tools for plotting methylation data in various ways
Methylation/modified base calling separated from basecalling.
A simplified version of Dorado built on top of S/BLOW5 format.
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023