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Unipro UGENE Manual, Version 1.20.0
Select the required parameters and press the Start button.
Building Index for BWA
To build BWA index select the Tools DNA Assembly Build Index item in the main menu. The Build Index dialog appears. Set the Align short
reads method parameter to BWA.
The dialog looks as follows:
There are the following parameters:
Reference sequence — DNA sequence to which short reads would be aligned to. This parameter is required.
Index file name — file to save index to. This parameter is required.
Index algorithm (-a) — Algorithm for constructing BWA index. Available options are:
It implements three different algorithms
is — designed for short reads up to ~200bp with low error rate (<3%). It does gapped global alignment w.r.t. reads, supports
paired-end reads, and is one of the fastest short read alignment algorithms to date while also visiting suboptimal hits.
bwtsw — is designed for long reads with more errors. It performs heuristic Smith-Waterman-like alignment to find
high-scoring local hits. Algorithm implemented in BWA-SW. On low-error short queries, BWA-SW. is slower and less
accurate than the is algorithm, but on long reads, it is better.
div — does not work for long genomes.
Colorspace (–color) — the input is read in colorspace, colors are encoded as characters A/C/G/T (A=blue, C=green, G=orange,
T=red).
BWA-SW
BWA is a fast light-weighted tool that aligns relatively short reads to a reference sequence. Click this link to open BWA homepage. BWA-SW
share similar features such as long-read support and split alignment. BWA-SW is embedded as an external tool into UGENE.
Open Tools Align to reference submenu of the main menu.
Select the Align short reads item to align short reads to a DNA sequence using BWA-SW. Or select the Build index item to build an index for
a DNA sequence which can be used to optimize aligning of short reads.
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