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bio-alignment-sorting
82 / 100 · Low risk
Fine to try.
By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
This is disclosed by the author in the skill's SKILL.md or README.
Found in 24 places.
Show 17 more
- skills/bioskills/alignment-sorting/SKILL.md, line 54
samtools sort -m 4G -@ 4 -o sorted.bam input.bam - skills/bioskills/alignment-sorting/SKILL.md, line 59
samtools sort -T /tmp/sort_tmp -o sorted.bam input.bam - skills/bioskills/alignment-sorting/SKILL.md, line 65
samtools sort -O bam -o sorted.bam input.bam - skills/bioskills/alignment-sorting/SKILL.md, line 74
samtools sort -t CB -o sorted_by_barcode.bam input.bam - skills/bioskills/alignment-sorting/SKILL.md, line 79
bwa mem ref.fa reads.fq | samtools sort -o aligned.bam - skills/bioskills/alignment-sorting/SKILL.md, line 93
samtools collate -O -u in.bam tmp_prefix | \ - skills/bioskills/alignment-sorting/SKILL.md, line 125
samtools view -H input.bam | grep "^@HD" - skills/bioskills/alignment-sorting/SKILL.md, line 134
samtools view input.bam | awk '$4 < prev {exit 1} {prev=$4}' - skills/bioskills/alignment-sorting/SKILL.md, line 181
subprocess.run( - skills/bioskills/alignment-sorting/SKILL.md, line 183
shell=True, check=True - skills/bioskills/alignment-sorting/SKILL.md, line 193
for f in *.bam; do samtools view -H "$f" | head -1; done | sort -u - skills/bioskills/alignment-sorting/SKILL.md, line 200
samtools merge -c -p -@ 8 merged.bam sample1.bam sample2.bam sample3.bam - skills/bioskills/alignment-sorting/SKILL.md, line 207
samtools merge -@ 4 merged.bam sample1.bam sample2.bam sample3.bam - skills/bioskills/alignment-sorting/SKILL.md, line 213
samtools merge -f merged.bam sample1.bam sample2.bam - skills/bioskills/alignment-sorting/SKILL.md, line 218
samtools merge -R chr1:1000000-2000000 merged_region.bam sample1.bam sample2.bam - skills/bioskills/alignment-sorting/SKILL.md, line 236
bwa mem -t 8 ref.fa R1.fq R2.fq | samtools sort -@ 4 -o aligned.bam - skills/bioskills/alignment-sorting/SKILL.md, line 243
samtools sort -n -o namesorted.bam input.bam
and 4 more places
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'bio-alignment-sorting' ] || [ -L ~/.agents/skills/'bio-alignment-sorting' ]; then echo 'A skill folder named bio-alignment-sorting 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 "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/bioskills/alignment-sorting' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioskills/alignment-sorting' ~/.agents/skills/'bio-alignment-sorting' && 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-sorting' ~/.claude/skills/'bio-alignment-sorting' (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 | 82 |