VAFがLoDスレスレで低クオリティの謎variantsがちょくちょく出るNGSパネル。塩基繰り返し領域の slippage を除外してもまだある。何らかの原因による頻発ノイズとして報告するため今まで走らせた検体情報をpythonか、さもなくばsamtoolsで一括見直しの必要があって情けない声が出そう　ヒイィー

10/ Real-world speed boost: I used parallel to run samtools mpileup on 50 BAMs. It saves time

17/ Action items: Learn STAR and BWA Practice samtools and bedtools Try making a BigWig file Visualize your data in IGV or UCSC browser

9/ Want a sorted BAM? Run: samtools sort file.bam -o file_sorted.bam Sorted files are faster for visualization and downstream tools.

8/ Use samtools to filter, sort, and index. Want to count properly aligned reads? Run: samtools view -c -F 4 file.bam

i should make a samtools repo...

They will claim the human sequences contaminating those metagenomic data are a privacy issue. But they could filter all human data out with samtools -f4 Just map the reads to human and post the unmapped bam file.

What matters less: memorizing samtools flags, writing boilerplate ggplot, debugging pandas indexing for the hundredth time.

gbdraw v0.10.0 webapp is now available!🧬 Major updates: 🔹Depth track support: Visualize your mapping depth simply by uploading samtools depth TSV files. 🔹Multithreaded LOSAT: Parallel execution to speed up multiple sequence comparisons. Check it out: gbdraw.app/

7/ Even tools like bedtools, bcftools, samtools rely on formats being clean. But they rarely are.

2/ Output: 1 2 ... 22 X Y Now replace echo with any command: samtools, bedtools, rsync—whatever your task is.

Week 1 was for Introduction to Linux for biologists. The concept of: • directories and files • command line basics • file ownership and file permissions • text editing/file manipulation • sort and uniq • grep • sed • awk • Environmental variables • Software Installation- Samtools 🙂‍↔️🤭

By the end of the weekend I had replaced all 15 QC tools in nf-core/rnaseq: dupRadar, featureCounts, RSeQC, preseq, samtools stats, Qualimap. RustQC produced all outputs with a single read of the BAM file. Time went from 15 hours to 15 minutes, >60x faster.

Introducing RustQC: 60x faster RNA-Seq quality control 🚀 We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in Rust: ✅ 15 h analyses → 15 min ✅ Identical outputs ✅ Drastically reduced I/O

I believe we can drive biomedicine forward by giving the right tools to the right people. That idea is what led me to build CRAM2Excel, a new HTSlib/SAMtools plugin that exports CRAM alignments directly into native Excel workbooks.

I built Genomix, an AI-powered CLI for DNA and genome analysis. Ask questions about your VCF, FASTA, FASTQ files in plain English. 9 MCP servers (samtools, BWA, GATK, BLAST , ClinVar...), works with Ollama, Claude, or OpenAI. Local-first by default your genomic data never leaves your machine. pip install genomix-cli github.com/hermias1/genomix-…

Release 1.23.1 of HTSlib, SAMtools, and BCFtools is now available from GitHub. This fixes crashes that could occur when reading malformed CRAM or GZI files. See htslib.org/download/ for links to tarballs and release notes.

9/ Samtools: Command-line utilities for manipulating BAM/SAM files. View, sort, index, and extract statistics from alignment files. Essential for anyone working with NGS data. samtools.github.io

🚀 Introducing TermiGen: Closing the Gap Between Open & Proprietary Terminal Agents Terminal tasks — system admin, DevOps, security forensics — are where AI agents meet the real world. And most open models fail here. Today, we're releasing: ✅ 32B model achieving 31.3% on TerminalBench 1.0 (new open-weight 32B SOTA) ✅ Beating o4-mini with Codex by 11.3% ✅ 3,500 verified Docker environments and tasks (covering 420 unique bash tools across 11 categories): 🛠️ System admin & DevOps (Docker, K8s, systemd) 🔐 Security & reverse engineering (Ghidra, Wireshark) 🧪 Scientific computing (samtools, GROMACS) 📊 8 more (ML, data processing, formal methods...) 📄 Paper: arxiv.org/abs/2602.07274 💻 3500 Env: github.com/ucsb-mlsec/termin… 🤖 Model: huggingface.co/UCSB-SURFI/Te…

【なぜLinuxが必要か】 NGS解析を本気でやろうとすると、避けて通れないのがLinux環境。 理由は単純で、主要なNGS解析ツールのほとんどが Linux前提で開発・配布されているから。 STARやsamtools、各種QCツールは、 Linux上で最も安定して動き、情報も圧倒的に多い。 WindowsやMacでも工夫すれば動かせるが、 その「工夫」に時間を取られがちになる。 それなら、最初からLinuxに慣れておくほうが良い。 幸いにも、Windows上で動作するWSLもある。 Linuxを学ぶ目的は、OSに詳しくなることではなくて、 解析を止めないための共通言語を手に入れること。 この視点で捉えると、Linuxはハードルではなく最短ルートになる。