BWA vs

Bowtie
Objectives

• Understand the BWA and Bowtie2 algorithm

• Basic statistics compare of both algorithms
• Difference of algorithm alignments results

BWA Bowtie2 BWA Bowtie2 BWA Bowtie2 BWA Bowtie2

Mapped by Both Mapped by One Mapped by None

FastQC Report
FastQC Report
Most Frequent Sequence in the FastQ
Count Sequence
152241 TAGAATAACATAGAATAACATAGAATAACATAGAATAACATAGAATAACAT

103593 AGCTTGCCTGGTAGGCGTCCACATCCAACAGTGCGGGAATGTTACCACCCT

89717 GAATAACATAGAATAACATAGAATAACATAGAATAACATAGAATAACATAG

89445 CAACACAACACAACACAACACAACACAACACAACACAACACAACACAACAC

78970 CATAGAATAACATAGAATAACATAGAATAACATAGAATAACATAGAATAAC

56690 TCGAGCAGGCAGAACGGGGTTCTGGAAAGCGACATCGGGGTAAAGTTTGAC

56187 CACAACACAACACAACACAACACAACACAACACAACACAACACAACACAAC

46895 AGAATAACATAGAATAACATAGAATAACATAGAATAACATAGAATAACATA

45937 ATAGAATAACATAGAATAACATAGAATAACATAGAATAACATAGAATAACA

42533 AGCTTAAAAGATGACACCGAACAGGGCGGGGATGGCGCAGGCGGCGGCAAC

41557 CGAGCAGGCAGAACGGGGTTCTGGAAAGCGACATCGGGGTAAAGTTTGACA

41078 AGCTTTTTTGAAAGTTAATCTCCTGGTTCACCGTCTGCTCGTACGCGGTTA

38363 ACACAACACAACACAACACAACACAACACAACACAACACAACACAACACAA

33951 ACATAGAATAACATAGAATAACATAGAATAACATAGAATAACATAGAATAA

30038 ATGTTATTCTATGTTATTCTATGTTATTCTATGTTATTCTATGTTATTCTA Unmapped

Read Flagstat
BWA Bowtie2
• 66695447 + 0 in total (QC-passed reads + QC-failed • 66690662 + 0 in total (QC-passed reads + QC-failed
reads) reads)
• 0 + 0 secondary • 0 + 0 secondary
• 4785 + 0 supplementary • 0 + 0 supplementary
• 0 + 0 duplicates • 0 + 0 duplicates
• 60200988 + 0 mapped (90.26% : N/A) • 59318895 + 0 mapped (88.95% : N/A)
• 0 + 0 paired in sequencing • 0 + 0 paired in sequencing
• 0 + 0 read1 • 0 + 0 read1
• 0 + 0 read2 • 0 + 0 read2
• 0 + 0 properly paired (N/A : N/A) • 0 + 0 properly paired (N/A : N/A)
• 0 + 0 with itself and mate mapped • 0 + 0 with itself and mate mapped
• 0 + 0 singletons (N/A : N/A) • 0 + 0 singletons (N/A : N/A)
• 0 + 0 with mate mapped to a different chr • 0 + 0 with mate mapped to a different chr
• 0 + 0 with mate mapped to a different chr • 0 + 0 with mate mapped to a different chr
(mapQ>=5) (mapQ>=5)
Read Count of Different aligner

Aligner Chromosome Count Percentage

bowtie2 chr3R 12369356 0.185460276
bowtie2 chr3L 10685860 0.160218733
bowtie2 chr2R 9405571 0.141022685
bowtie2 chr2L 9008972 0.135076267
bowtie2 chrY 926549 0.013892238
bowtie2 chrX 7843077 0.117595388
bowtie2 * 7371767 0.110528789
bowtie2 Random 9084295 0.136205624
bwa chr3R 12519277 0.187721588
bwa chr3L 10880591 0.163150142
bwa chr2R 9554136 0.143260476
bwa chr2L 9167088 0.137456845
bwa chrY 916787 0.013746857
bwa chrX 7867952 0.117976817
bwa * 6494459 0.097381834
bwa Random 9290372 0.13930544
 Mapped by None

BWA Bowtie
2
Mapped by
None

Mapped by None

Original Fastq

Mapped by None
 Read Depth Chr3R

bowtie2

bwa
 Read Depth Chr3R
10K Moving Avg

bowtie2

bwa
 Read Depth Chr3L

bowtie2

bwa
 Read Depth Chr3L
10K Moving Avg

bowtie2

bwa
 Read Depth ChrX

bowtie2

bwa
 Read Depth ChrX
10K Moving Avg

bowtie2

bwa