SeqKit

VSEARCH — open-source, multithreaded alternative to USEARCH for amplicon and metagenomics sequence analysis. Performs dereplication, chimera detection (de novo and reference-based), OTU/ASV clustering

2 shared topics • 1 shared operation

MicrobiomeAnalystR — comprehensive R package for statistical analysis of microbiome data from 16S rRNA amplicon sequencing and shotgun metagenomics. Provides alpha diversity (Shannon, Chao1, ACE, Fait

2 shared topics

Sylph — ultrafast metagenomic profiling and containment ANI estimation using k-mer sketching. Performs species-level taxonomic profiling with abundance quantification and genome querying against pre-b

2 shared topics

treeio — Bioconductor R package for importing and exporting phylogenetic tree data with associated metadata. Reads and writes Newick, Nexus, BEAST, RAxML, FastTree, IQ-TREE, MrBayes, PHYLODOG, r8s, ME

2 shared topics

ballgown -- R/Bioconductor package for flexible isoform-level differential expression analysis of RNA-seq experiments. Works with StringTie output (.ctab files) to test for differential expression at

1 shared topic • 1 shared operation