Explore tweets tagged as #minimap2
Accelerating whole-genome alignment in the age of complete genome assemblies ロングリードの高速アライナーminimap2の精度を維持したまま、更に高速化したmm2-plus。mimimap2と同じオプションが利用可能。 https://t.co/9dsgAQEvEf
https://t.co/NHuvU2vYZ0
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Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. https://t.co/aLB9juf08k
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#NanoporeConf Data for Breakfast Q&A Dorado will continue to support 4kHz; MinKNOW will switch to 5kHz Dorado aligner doesn’t support spliced alignment - but working on it Ont preset in minimap2 may not make sense anymore - exploring best parameters
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A concise description of part of the philosophy behind many of @lh3lh3's tools, made in response to the question of why minimap2 only outputs SAM & not BAM format directly. Managing software design is hard, & balances between immediate features and code & maintenance complexity.
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Nanocount- EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2 https://t.co/1qvqz3pa1p
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A meticulous effort by @kisarul in integrating FPGA-accelerated chaining into Minimap2 https://t.co/2q2Ez2XnLe Mapping accuracy is near identical. end-to-end runtime improves ~10-80% (depend on type of data/parameters). code+pre-built aws binaries https://t.co/9GGsRtjaEu
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A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies. For ONT lrWGS, alignment with minimap2-among four aligners tested-consistently led to the best results. At up to 10× coverage, Duet achieved the highest
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chatgptにminimap2のオプションがどうなってるかコードを貼り付けながら聞いている。合ってるかどうかはともかく、バイオインフォの家庭教師って感じはある。
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Alaina Shumate follows at the #Bioinformatics session at #PAG30 with LiftoffTools to compare genome annotations mapped between genome assemblies. Compare gene models is a more complex problem than just convert coordinates. Liftoff uses Minimap2 to map gene models.
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Old‑school aligners just got a neural copilot 🚁 Drop minisplice into minimap2/miniprot → 3× fewer bad junctions on noisy reads, cross‑species mapping unlocked 🔓 Tiny CNN, outsized impact 📈
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Checkout minimap2-fpga, a fork of minimap2 that integrates fpga accelerated changing part, which is now published at https://t.co/p0IRUuanPZ
Thrilled to share that our paper on minimap2-fpga is now published in Nature Scientific Reports! https://t.co/e1dprzRJDT Our end-to-end integration of FPGA hardware accelerator for chaining enhances Minimap2's runtime by ~10-80%. Mapping accuracy remains near-identical.
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a जीनोम फास्टा minimap2 Minimap2 अनुक्रमणिका minimap2 पढ्छ जेनरिक पीक्स बेड ओछ्यान उपकरणहरू शिखर फास्टा kallisto kallisto सूचकांक BAM शिखर खोज कल्लीस्टो बुस्टुलहरू गणना गर्छ म्यापिङ पढ्नुहोस्
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minimap2 を更新したら、covermでdepth を計算しようとするとエラーを吐くようになってしまって困ったなと思っていたが、samtools coverageでもっと速くしかもより多くの情報が得られるということを知る。 samtools coverage <input.bam>
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PacBio/ONTのロングリードを対象としたメタゲノムの系統分類ツールの比較 - タンパク質変換するツールはダメ - kmerベースのツールがいい - kraken2, minimap2, Ramが良い結果 - シーケンスリードは長さより精度 - ホスト多寡のサンプルは通常サンプルと傾向が異なる
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Got a chance to take the @nanopore hyp(er accuracy) model for a spin. Pretty decent improvement in read quality 🚀 but expect to spend quite some more GPU hours 😉 (Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)
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