Long Reads Python Packages

pyabpoa

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

strkit

A short tandem repeat (STR) genotyping and analysis toolkit for long reads

biolic

Placeholder for biolic, a fast streaming bioinformatics toolkit. Python bindings are planned; the tool currently ships as a Rust CLI.

isocon

Pipeline for obtaining non-redundant haplotype specific transcript isoforms using PacBio IsoSeq reads.

pepper-polish

PEPPER-Margin-DeepVariant

lapa

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

tiptoft

Predict plasmids from uncorrected long read data

pyscaf

Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.

plasmidpredictor

Predict plasmids from uncorrected long read data