| name | pilon |
| description | Polish genome assemblies and fix small errors using short-read BAM evidence. Use after mapping Illumina reads to a draft assembly (including long-read drafts). Upstream: https://github.com/broadinstitute/pilon.
|
| license | MIT |
| category | analysis-tools |
| tags | ["polish","assembly","short-read"] |
| upstream | https://github.com/broadinstitute/pilon |
| stage | assembly |
Pilon
Upstream: broadinstitute/pilon
Citation
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial
variant detection and genome assembly improvement. PLoS ONE 9, e112963
(2014). https://doi.org/10.1371/journal.pone.0112963
Analytical thinking
Pilon uses short-read alignments to correct SNPs/indels and optionally fill
gaps. Requires high-quality BAM (Bowtie2/BWA) to the draft. Over-polishing
heterogeneous metagenome contigs can erase true strain variation — prefer on
isolate-like MAGs or low-complexity drafts, not blindly on all community
contigs.
How to run
conda install -c bioconda pilon bowtie2 samtools
bowtie2-build draft.fa temp/polish/draft
bowtie2 -x temp/polish/draft -1 R1.fq.gz -2 R2.fq.gz -p 16 \
| samtools sort -@ 8 -o temp/polish/illumina.bam
samtools index temp/polish/illumina.bam
pilon --genome draft.fa --frags temp/polish/illumina.bam \
--output draft.pilon --outdir temp/polish --threads 16
Related skills
bowtie2 · samtools · racon · quast · megahit · metaflye
