SciPy

Pychopper — Nanopore direct cDNA read preprocessing tool that identifies, orients, and trims full-length reads using primer detection (pHMM or alignment). Rescues fused reads by dynamic programming, e

2 shared topics • 1 shared operation

RTG Tools — Java-based toolkit from Real Time Genomics for haplotype-aware variant call comparison, VCF filtering, statistics, and pedigree analysis. Primary use: vcfeval for benchmarking variant call

2 shared topics • 1 shared operation

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 • 2 shared operations

Use when performing differential gene expression analysis on RNA-seq count data using limma-voom. Covers the full workflow: count filtering with filterByExpr, TMM normalization via edgeR calcNormFacto

1 shared topic • 2 shared operations

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

1 shared topic • 2 shared operations