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Result file name — file in SAM format to write the result of the alignment into. This parameter is required.Prebuilt index — check this box to use an index file instead of a source reference sequence. Also you can build it manually.
SAM output — always save the output file in the SAM format (the option is disabled for BWA).
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You can also configure other parameters.
Index algorithm (-a) — algorithm for constructing BWA-SW index.
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.
Score for a match (-a) — score of a match.
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Band width (-w) - Band width in the banded alignment.Mask level (-c) - Coefficient for threshold adjustment according to query length. Given an l-long query, the threshold for a hit to be retained is a*max{T,c*log(l)}.
Number of threads (-t) - Number of threads in the multi-threading mode.
Size of chunk of reads (-s) - Maximum SA interval size for initiating a seed. Higher -s increases accuracy at the cost of speed.
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Number of seeds to start rev alignment (-N) - Minimum number of seeds supporting the resultant alignment to skip reverse alignment.
Mask level (-c) - Coefficient for threshold adjustment according to query length. Given an l-long query, the threshold for a hit to be retained is a*max{T,c*log(l)}.
Prefer hard clipping in SAM output (-H) - use hard clipping in the SAM output. This option may dramatically reduce the redundancy of output when mapping long contig or BAC sequences.
Select the required parameters and press the Start button.