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/softwares_database/bwa.txt
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| a | b/softwares_database/bwa.txt | ||
|---|---|---|---|
| 1 | 1. install |
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| 2 | mamba install bwa |
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| 3 | |||
| 4 | 2. build index |
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| 5 | bwa index <path to reference genome file> |
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| 6 | |||
| 7 | 3. alignment with single-end reads |
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| 8 | bwa mem <path to reference genome file> <path to reads file> > <path to output sam file> |
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| 9 | |||
| 10 | 4. alignment with paired-end reads |
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| 11 | bwa mem <path to reference genome file> <path to read 1 file> <path to read 2 file> > <path to output sam file> |
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| 12 | |||
| 13 | 5. alignment with PacBio subreads |
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| 14 | bwa mem -x pacbio <path to reference genome file> <path to reads file> > <path to output sam file> |
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| 15 | |||
| 16 | 6. alignment with Oxford Nanopore reads |
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| 17 | bwa mem -x ont2d <path to reference genome file> <path to reads file> > <path to output sam file> |