List of parameters present in Bowtie and BWA aligners

Here is a complete list of some important parameters used in both aligners to control the alignment of FastQ data.

BWA		Bowtie
Parameter	Description	Parameter	Description
Bwa alignment options	There are different parameters for alignment which are listed below	-u 20	This option causes Bowtie to exit after processing first 20 reads from file
-n NUM	Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT	-S	To obtain alignment in SAM format
-o INT	Maximum number of gap opens	-l	To confirm that output files are created
-e INT	Maximum number of gap extensions	--suppress	Suppresses all outputs if columns number is not mentioned otherwise suppresses the mentioned columns
-a STR	Algorithm for constructing BWT index	-a	Instructs bowtie to report all valid alignments subject to the alignment policy
-d INT	Disallow a long deletion within INT bp towards the 3’-end	-k	Reports all the valid alignments
-i INT	Disallow an indel within INT bp towards the ends	--best	Guarantees that bowtie will find and print the alignments for a given read in best-to-worst order
-p STR	Prefix of the output database	-p	Value greater than 1 allows bowtie to use more than computer processor
-l INT	Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled.	--offrate	Adjusts the error message about memory having been exhausted
-k INT	Maximum edit distance in the seed	-C	Enables alignment of color space reads produced by ABI SOLiD
-t INT	Number of threads (multi-threading mode)	-v <int>	Only alignment up to <int> mismatches in the entire alignment are considered “valid”
-O INT	Gap open penalty	-n <int>	Only alignment with up to <int> mismatches in the seed portion of alignment are considered “valid”
-I	The input is in the Illumina 1.3+ read format (quality equals ASCII-64)	-l <int>	When -n is specified, -l sets the length of the seed portion of the alignment to <int>
-E INT	Gap extension penalty	-e <int>	When -n is specified, -e sets the limit
-b	Specify the input read sequence file is the BAM format. For paired-end data, two ends in a pair must be grouped together and options -1 or -2 are usually applied to specify which end should be mapped.	-m <int>	If bowtie finds more than <int> valid arguments for a read, suppress all alignments for a read
-M INT	Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc)	-M <int>	If bowtie finds more than <int> valid alignments for a read, suppress the alignments but report one of them at random
samse	Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.	-1	-1 is specified for single end alignment
sampe	Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.	-2	Specified for paired end alignment