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