npm

polypolish

Polish long-read assemblies using short-read sequencing data

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About

Short-read polishing tool for long-read assemblies

Commands

polypolish

Examples

Polish an assembly using paired-end short reads$ polypolish --assembly assembly.fasta --short_reads reads_1.fastq reads_2.fastq --output polished.fasta
Polish assembly with multiple read files and specify threads$ polypolish --assembly long_read_assembly.fasta --short_reads set1_R1.fastq set1_R2.fastq set2_R1.fastq set2_R2.fastq --threads 8 --output polished_assembly.fasta
Run polishing with verbose output to monitor progress$ polypolish --assembly draft.fasta --short_reads reads_1.fastq reads_2.fastq --verbose --output result.fasta