What it does Polypolish is a tool for polishing genome assemblies with short reads. Polypolish uses SAM/BAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.

Polypolish pipeline steps 1. [Optional] Filter aligned reads Exclude some alignments based on their insert size This should reduce the number of excessive alignments, particularly near the edges of repeat sequences, improving Polypolish's ability to fix errors in those regions. 2. Clean assembly with filtered reads

Inputs Polypolish need SAM/BAM input format obtain from aligner with option to keep all possible location Polypolish take on or more assembly as input fasta. It need also raw data reads in single or paired-end SAM/BAM format. You can use multiple aligned data to polish the same assembly. WARNING It can only work if multiple location information is available in sam/bam files For example using bwa mem to align raw data before use, you need : 1. To align each read data independantly (also for paired data) 2. Set the option "Output all alignments for single-ends or unpaired paired-ends" in Select analysis mode>Set input/output options This allow multiple ailgnemnt output need to use polypolish