Long Read Sequencing Python Packages

deepchopper-cli

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

deepchopper

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

dajin2

🔬 Genotyping tool for genome-edited samples using nanopore-targeted sequencing

strkit

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

midsv

a Python module to translate SAM into MIDSV format.

atarva

ATaRVa - Analysis of Tandem Repeat Variation

nanome-jax

NANOME (Nanopore methylation) pipeline developed by Li Lab at The Jackson Laboratory

stranger

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

biolic

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

altanalyze3

AltAnalyze3: Advanced RNA-Seq Analysis Workflow

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

ultra-bioinformatics

Splice aligner of long transcriptomic reads to genome.

jaffatools

A Python toolkit for JAFFA fusion gene detection