Long Read Sequencing Python Packages

midsv

a Python module to translate SAM into MIDSV format.

dajin2

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

strkit

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

deepchopper-cli

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

octopusv

Merge and compare structural variants across callers, samples, and platforms. Standardizes BND-heavy output from GRIDSS, SvABA, Sniffles, and more.

atarva

ATaRVa - Analysis of Tandem Repeat Variation

deepchopper

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

pie-phasing-eval

Phasing all-In-one Evaluator

stranger

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

nanome-jax

NANOME pipeline (Nanopore long-read sequencing consensus DNA methylation detection method and pipeline)

altanalyze3

AltAnalyze version 3 is a Python3 library to integrate and compare diverse RNA isoform datasets.

ultra-bioinformatics

Long-read splice alignment with high accuracy

deepconsensus

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

nanofetch

Extracts gene-centered BAMs in seconds by gene name, panel, or genome build, from GRCh37 to T2T.

biolic

A fast, modular, streaming bioinformatics toolkit in Rust for FASTQ/FASTA/BAM — a platform that grows through modules, with strong long-read support.

scanmst

A multi-segment transcript caller for long-read transcriptome sequencing data

jaffatools

A Python toolkit for JAFFA fusion gene detection

vmwhere

exploring microsatellites in the human genome

strainy

Graph-based assembly phasing