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bio-alignment-filtering
75 / 100 · Review before installing
Check before installing.
By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 22 places.
Show 17 more
- skills/bioskills/alignment-filtering/SKILL.md, line 73
samtools view -F 1024 -o nodup.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 78
samtools view -F 2304 -o primary.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 83
samtools view -F 256 -F 2048 -o primary.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 89
samtools view -f 64 -o read1.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 94
samtools view -f 128 -o read2.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 99
samtools view -F 16 -o forward.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 104
samtools view -f 16 -o reverse.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 111
samtools view -q 30 -o highqual.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 116
samtools view -F 4 -q 30 -o filtered.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 136
samtools view -q 1 in.bam # exclude MAPQ=0; works for all aligners - skills/bioskills/alignment-filtering/SKILL.md, line 143
samtools view -o region.bam input.bam chr1:1000000-2000000 - skills/bioskills/alignment-filtering/SKILL.md, line 148
samtools view -o regions.bam input.bam chr1:1000-2000 chr2:3000-4000 - skills/bioskills/alignment-filtering/SKILL.md, line 153
samtools view -L targets.bed -o targets.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 158
samtools view -q 30 -L targets.bed -o filtered.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 171
samtools view -F 3332 -q 30 -o filtered.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 197
samtools view -f 2 -F 3328 -q 20 -o clean.bam input.bam - skills/bioskills/alignment-filtering/SKILL.md, line 219
samtools view -s 42.1 -b -o subset.bam input.bam
and 2 more places
Connects to the internet
The author does not mention this.
Found in 3 places.
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Safer alternatives
Low-risk skills in the same category (design) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'bio-alignment-filtering' ] || [ -L ~/.agents/skills/'bio-alignment-filtering' ]; then echo 'A skill folder named bio-alignment-filtering already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/bioskills/alignment-filtering' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioskills/alignment-filtering' ~/.agents/skills/'bio-alignment-filtering' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-alignment-filtering' ~/.claude/skills/'bio-alignment-filtering' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for BioTender-max/awesome-bio-agent-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/BioTender-max/awesome-bio-agent-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 8cbdd18 | 75 |