pybio: bioinformatics and genomics manipulations
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README.md

pybio: basic genomics toolset

pybio is a Python framework for basic genomics operations. The package is a dependency to apa (alternative polyadenylation) and RNAmotifs2 (motif cluster analysis). The pybio package provides:

  • automatized download of genome assemblies from Ensembl and STAR indexing,
  • automatized download of genome annotations from Ensembl GTF with fast-searching capabilities,
  • Fasta, Fastq, bedGraph and other file format handling,
  • motif sequence searches,
  • alternative polyadenylation site-pair classification (same-exon, skipped-exon, composite-exon),
  • and other.

Authors

pybio is developed and supported by Gregor Rot.

Reporting problems

Use the issues page to report issues and leave suggestions.