Welcome to your wiki!
This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
The wiki uses Markdown syntax.
If you need help with installing and running Swift, please contact Pankaj Gupta at email@example.com.
$ tar -xvzf swift-x.y.z.tar.gz
$ cd /path/to/swift-x.y.z
$ /path/to/swift -q \<query fasta file> -r \<reference fasta file> -o \<output file>
-q2 \<string> Paired query fasta file
-l \<int> Length of seed (Default: 12)
-m \<int> Match score (Default: 2)
-M \<int> Mismatch score (Default: -1)
-O \<int> Gap open penalty (Default: -10)
-E \<int> Gap extension penalty (Default: -1)
-t \<int> Threshold value to ignore reference repeats
-cpu Run program on CPU only
-f \<int> Output format:
0 - Default alignment output format. Output includes alignment, score, positions, and length.
1 - SAM format
-v Print program version
-h Print usage
Q: Is there a limit on the number of reference sequences that can be used in Swift?
A: Yes, currently Swift supports 25 or so reference sequences due to memory limitations on the GPU.
Q: Is there a limit on the size of each reference sequence?
A: No, there is no limit on the size of each reference sequence. However, there is a limit on the number of reference sequences.
Q: What Operating Systems is Swift available for?
A: Currently Swift is available for Linux OS only.
Q: Under what license is Swift available?
A: Swift is available under GPLv2 license.
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