## A5 assembly pipeline for microbial genomes

### Description

Construct small genomes based on the Illumina MiSeq data.

This tool runs A5-miseq pipeline that is designed for assembling DNA sequence data generated on the Illumina sequencing platform. There are many situations where A5-miseq is not the right tool for the job. In order to produce accurate results, A5-miseq requires Illumina data with certain characteristics. A5-miseq will likely not work well with Illumina reads shorter than around 80 nt, or reads where the base qualities are low in all or most reads before 60 nt. A5-miseq assumes it is assembling homozygous haploid genomes. Use a different assembler for metagenomes and heterozygous diploid or polyploid organisms. Use a different assembler if a tool like FastQC reports your data quality is dubious.

The tool needs a pair of fastq formatted paired-end reads files.

For more details, please check the home page of A5-miseq pipeline and the PLOS One article about the A5 miseq pipeline.

### Output

- a5_assembly.contigs.fasta: Contigs
- a5_assembly.final.scaffolds.fasta: Final scaffolds (checked for misassemblies, and rescaffolded).
- a5_assembly.final.scaffolds.fastq: Final scaffolds in FastQ format with base call qualities.
- a5_assembly.final.scaffolds.qvl: Quality values for the final scaffolds in QVL format for submission to NCBI.
- a5_assembly_stats.csv: A tab-separated file with assembly summary statistics.