Biopython SeqIO

Augur — Nextstrain's Python toolkit for phylogenetic analysis of pathogen genomes. Provides modular subcommands for sequence filtering, multiple alignment, phylogenetic tree building, temporal dating,

1 shared topic • 1 shared operation

Use when working with csvtk — csvtk — cross-platform, ultrafast CSV/TSV

1 shared topic • 1 shared operation

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

1 shared topic • 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

1 shared topic • 1 shared operation

Use when working with SciPy — the foundational Python scientific computing library — for statistical testing, signal processing, optimization, linear algebra, spatial analysis, and numerical integrati

1 shared topic • 1 shared operation