crazyhottommy/awesome-long-reads

tools and notes for long reads analysis

awesome-long-reads

tools and notes for long reads analysis

• awesome-nanopore
• https://labs.epi2me.io/ oxford Nanopore dataset and tutorials
• https://labs.epi2me.io/dataindex/

slow5curl is a command line tool and a library and for fetching reads from remote BLOW5 files, which is built on top of slow5lib and libcurl.

Variant

• Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

• Pipeline is Dorado, minimap2, sniffles2, deepvariant, you can do it under 1 hour now https://x.com/erictdawson/status/1710118874300219881?s=20 https://developer.nvidia.com/blog/boosting-ultra-rapid-nanopore-sequencing-analysis-on-nvidia-dgx-a100/

• Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads: https://github.com/nanoporetech/dorado

pipeline: Mapping: Minimap2 or NGMLR SNVs: Clair3 SVs: Sniffles2 Phasing SNVs: WhatsHap Phasing SVs: Sniffles2 Extend Phasing: PRINCESS-subtool Phased Methylation: Nanopolish + PRINCESS-subtool QC Statistics for each step

https://github.com/MeHelmy/princess and https://github.com/epi2me-labs/wf-human-variation

• Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT).

• CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution https://www.biorxiv.org/content/10.1101/2024.02.24.581862v1.full

• Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads https://www.biorxiv.org/content/10.1101/2024.02.26.582089v1

DNA methylation.

• Mehtylartist Tools for parsing and plotting methylation patterns from nanopore data

RNA isoform

• ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data

RNA modification

• Enhanced detection of RNA modifications and mappability with high-accuracy nanopore RNA basecalling models