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alignment-filtering
75 / 100 · Review before installing
Check before installing.
By mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- (GitHub) · other · 36 stars · scanned at commit fde6cd1
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 21 places.
Show 17 more
- Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 75
samtools view -F 1024 -o nodup.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 80
samtools view -F 2304 -o primary.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 85
samtools view -F 256 -F 2048 -o primary.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 91
samtools view -f 64 -o read1.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 96
samtools view -f 128 -o read2.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 101
samtools view -F 16 -o forward.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 106
samtools view -f 16 -o reverse.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 113
samtools view -q 30 -o highqual.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 118
samtools view -F 4 -q 30 -o filtered.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 135
samtools view -o region.bam input.bam chr1:1000000-2000000 - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 140
samtools view -o regions.bam input.bam chr1:1000-2000 chr2:3000-4000 - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 145
samtools view -L targets.bed -o targets.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 150
samtools view -q 30 -L targets.bed -o filtered.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 158
samtools view -F 3332 -q 30 -o filtered.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 165
samtools view -f 2 -F 3328 -q 20 -o clean.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 173
samtools view -F 1024 -q 30 -o filtered.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-filtering/SKILL.md, line 181
samtools view -s 0.1 -o subset.bam input.bam
and 1 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 (other) 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/'alignment-filtering' ] || [ -L ~/.agents/skills/'alignment-filtering' ]; then echo 'A skill folder named alignment-filtering already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-' "$d" && git -C "$d" checkout --quiet 'fde6cd1025d8a9300ad783b3d6696fa708a5cdb0' -- 'Skills/Sequence_Analysis/alignment-files/alignment-filtering' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Sequence_Analysis/alignment-files/alignment-filtering' ~/.agents/skills/'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/'alignment-filtering' ~/.claude/skills/'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 mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-/)
Score history
| Date | Version | Score |
|---|
| 2026-11-13 | fde6cd1 | 75 |
| 2026-11-07 | 839c35a | 75 |