bio-genome-assembly-assembly-polishing

npx skills add BioTender-max/awesome-bio-agent-skills --skill assembly-polishing --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: BWA 0.7.17+, QUAST 5.2+, minimap2 2.26+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Assembly Polishing **"Polish my genome assembly"** → Iteratively correct base-level errors in a draft assembly using short-read or long-read alignments. - CLI: `pilon --genome draft.fa --frags short_reads.bam` (short-read), `medaka_polish` (ONT), `racon` (long-read) ## Polishing Strategies | Tool | Input Reads | Best For | |------|-------------|----------| | Pilon | Illumina | Final polishing | | medaka | ONT | ONT assemblies | | Racon | Long reads | Quick polishing | | NextPolish | Both | Combined approach | ## Recommended Workflows ### ONT Assembly 1. Racon (2-3 rounds with ONT) 2. medaka (1 round) 3. Pilon (2-3 rounds with Illumina) ### PacBio CLR Assembly 1. Racon (2-3 rounds) 2. Pilon (2-3 rounds with Illumina) ### PacBio HiFi Assembly - Often no polishing needed (>

conda install -c bioconda pilon
Map short reads to assembly
bwa index assembly.fasta
bwa mem -t 16 assembly.fasta R1.fq.gz R2.fq.gz | samtools sort -o aligned.bam
samtools index aligned.bam
Run Pilon
pilon --genome assembly.fasta --frags aligned.bam --output polished
for i in $(seq 1 $ROUNDS); do
echo "=== Pilon round $i ==="
bwa index $current