Mapping - BBmap & Samtools

(conda)

◆ Install

>>> conda install bioconda::bbmap

>>> conda install bioconda::samtools

 

◆ Usage

1. Reference Index

>>> bbmap.sh -Xmx32g ref=reference.fasta

 

2. Mapping(Illumina)

>>> bbmap.sh -Xmx32g in1=input_fwd.fastq in2=input_rev.fastq out=output_mapped.sam

 ref=reference.fasta

 

3. Sam -> Bam 변환

>>> samtools view -Sb output_mapped.sam > output_mapped.bam

 

4. Sort 

>>> samtools sort -o output_sorted.bam output_mapped.bam

 

5. Bam Index - .bai 생성

>>> samtools index output_sorted.bam