notepad.md

Comparing bwa and magicblast

We downloaded the read sets and reference genomes for E. coli ST131 (SRR5629778 and HG941718.1) and Homo sapiens (SRR2848544 and GRCh38.p7 Primary Assembly). Each read set was aligned against its own reference genome and the opposing reference using bwa 0.7.12-r1039 and ncbi-magicblast-1.3.0.

Self-comparison

E.coli

total reads

grep "@SRR5629778" SRR5629778.ecoli.st131.fastq |wc
10964

bwa:

mapped reads

samtools view -bS SRR5629778_bwa.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
7581

unmapped reads

samtools view -bS SRR5629778_bwa.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
3383

magicblast:

mapped reads

samtools view -bS SRR5629778_magicblast.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
9919

unmapped reads

samtools view -bS SRR5629778_magicblast.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
1045

Homo sapiens

total reads

grep "@SRR2848544"  ~/bastian/reference_data/SRR2848544.fastq |wc
2912

bwa:

mapped reads

samtools view -bS SRR2848544_bwa.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
2910

unmapped reads

samtools view -bS SRR2848544_bwa.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
2

magicblast:

mapped reads

samtools view -bS SRR2848544_magicblast_default.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
2912

unmapped reads

samtools view -bS SRR2848544_magicblast_default.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
3

Cross comparison

E. coli reads against Homo sapiens

bwa:

mapped reads

samtools view -bS SRR5629778.ecoli.st131_bwa.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
0

unmapped reads

samtools view -bS SRR5629778.ecoli.st131_bwa.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
10964

magicblast:

mapped reads

samtools view -bS SRR5629778.ecoli.st131_magicblast.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
10955

unmapped reads

samtools view -bS SRR5629778.ecoli.st131_magicblast.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
9

Homo sapiens reads against E. coli

bwa:

mapped reads

samtools view -bS SRR2848544_bwa_he.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
0

unmapped reads

samtools view -bS SRR2848544_bwa_he.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
2912

magicblast:

mapped reads

samtools view -bS SRR2848544_magicblast_he.sam |samtools view -F 4 -|cut -f 1|sort|uniq |wc -l
292

unmapped reads

samtools view -bS SRR2848544_magicblast_he.sam |samtools view -f 4 -|cut -f 1|sort|uniq |wc -l
2899

How-to run bwa

Create index of the reference genome:

bwa index reference_genome.fasta reference_genome.fasta

Align reads

bwa mem reference_genome.fasta read_set.fastq