API reference

The Python API of Sequana is broken into themed sections. Each page is an exhaustive listing generated with Sphinx autodoc.

• References (IO / file formats)
  • FASTA
  • FASTQ
  • BED / wig / mpileup
  • GFF / GTF / GenBank / GFA
  • VCF
  • Other formats
• References (genomics: sequences, motifs, RNA)
  • Sequence basics
  • Regulatory / regulatory-adjacent
  • Non-B DNA / motif detection
  • RNA structure & rRNA depletion
• References (pipeline back-ends)
  • BAM / alignment
  • Coverage
  • Assembly and contigs
  • Taxonomy
  • PacBio / IsoSeq / LAA
  • RNA-seq / counting
  • Variants / annotation
  • ChIP-seq / peak calling
  • Wrappers to other tools
  • Module reports
• References (utilities and misc)
  • General tools
  • Test data and discovery
  • sequana.utils
  • sequana.plots
• References (enrichment)
  • Enrichment tools
• References (stats)
  • Statistical tools
• References (Viz)
  • Visualisation