shovill 使用

Main steps : 

1. Estimate genome size and read length from reads (unless --gsize provided)

2. Reduce FASTQ files to a sensible depth (default --depth 100)

3. Trim adapters from reads (with --trim only)

4. Conservatively correct sequencing errors in reads

5. Pre-overlap ("stitch") paired-end reads

6. Assemble with SPAdes/SKESA/Megahit with modified kmer range and PE + long SE reads

7. Correct minor assembly errors by mapping reads back to contigs

8. Remove contigs that are too short, too low coverage, or pure homopolymers

9. Produce final FASTA with nicer names and parseable annotations

优点：组装前有reads纠错；组装后也有纠错，可以根据contig长度对数据进行去除。

使用脚本：shovill --R1 aaa1.fq --R2 aaa2.fq -- outdir outpath  --cpus 16  --depth 0 --minlen 100 --ram 20