Automate QC, trimming, alignment, and BAM processing for sequencing data.
npx skills add https://github.com/ClawBio/ClawBio --skill seq-wrangler
Please help me install this Agent Skill. Skill: seq-wrangler Source: https://github.com/ClawBio/ClawBio/tree/main/skills/seq-wrangler Command: npx skills add https://github.com/ClawBio/ClawBio --skill seq-wrangler
Seq Wrangler automates the repetitive, multi-step tasks required to turn raw sequencing reads into analysis-ready BAM files, eliminating manual orchestration of QC, trimming, alignment, and BAM processing across samples.
Run QC on sample_R1.fastq/sample_R2.fastq, trim adapters, align to GRCh38, and produce a sorted, indexed BAM plus a MultiQC report.
High-intent search queries and answers about installing and using this skill.
To process raw sequencing reads into sorted and indexed BAM files, the pipeline applies QC, adapter trimming, and alignment using BWA or Bowtie2. It then sorts, indexes, and marks duplicates using samtools to generate analysis-ready BAM files.
The best way to generate MultiQC reports for paired-end Illumina samples is to run FastQC for initial read quality control. The workflow then aggregates these results into a MultiQC summary to identify quality issues across libraries.
Yes, this workflow supports long-read sequencing data alignment. You can align long-read datasets using Minimap2, then sort, index, mark duplicates, and compute coverage with samtools to produce analysis-ready BAM files.
Yes, you need samtools and at least one aligner such as BWA, Bowtie2, or Minimap2. Optionally, you can use FastQC, fastp, MultiQC, and Picard for read quality control, adapter trimming, and duplicate marking during BAM processing.
Yes, you can export Nextflow pipelines and environment specifications for sequence alignment. The workflow generates reproducible shell scripts and exports checksums to ensure full reproducibility of the read processing and BAM generation steps.
MubasherMohammedAutomate NGS read alignment and processing from FASTQ to BAM.
Lord1EgyptRead and manipulate SAM, BAM, CRAM, VCF, and BCF genomic files.
awslabsOrchestrate FastQC, fastp, samtools, and Picard for Illumina sequencing QC.
abrahamgreysonAutomate GSD project initialization and planning with a step-by-step workflow.
