Tuesday, 25 April 2017

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 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
To obtain alignment in SAM format

-o INT
Maximum number of gap opens
To confirm that output files are created
-e INT
Maximum number of gap extensions
Suppresses all outputs if columns number is not mentioned otherwise suppresses the mentioned columns
-a STR
Algorithm for constructing BWT index
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 

Reports all the valid alignments
-i INT
Disallow an indel within INT bp towards the ends
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
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.
Adjusts the error message about memory having been exhausted
-k INT
Maximum edit distance in the seed
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”
Gap open penalty
-n <int>
Only alignment with up to <int> mismatches in the seed portion of alignment are considered “valid”

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>

Gap extension penalty
-e <int>
When -n is specified, -e sets the limit
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
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
Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.
-1 is specified for single end alignment
Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
Specified for paired end alignment