Metagenomic assembly and binning pipeline for Beck Research Lab

Generalized protocol

• Trim (see separate protocol repo)
• Initial assembly
  • Use all reads from all libraries
  • PE reads are used as pairs, SE as singletons
• Map raw (untrimmed) reads back to contigs for coverage
• Bin with metabat
  • Successive rounds of binning with parameter searches
  • Choose bins with best precision / recall #s
• Map trimmed reads back to contigs for individual bins
• Extract mapped reads
  • Include pairs, even if unmapped
• Reassemble bins with mapped reads using spades

Required software

• anaconda3
• bam-readcount
• bedtools
• blast
• bowtie2
• bwa
• checkm
• CONCOCT
• DESMAN
• diamond
• hmmer
• megahit
• metabat
• parallel
• picard
• pplacer
• prodigal
• pysam
• R
• samtools
• spades