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/softwares_database/bowtie2.txt
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| a | b/softwares_database/bowtie2.txt | ||
|---|---|---|---|
| 1 | 1. Install the bowtie2 |
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| 2 | mamba install -c bioconda bowtie2 -y |
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| 3 | |||
| 4 | 2. Build an index using bowtie2 |
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| 5 | bowtie2-build --threads <number of alignment threads to launch> <path to genome fasta file> <path to Index filename prefix (minus trailing .X.bt2)>> |
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| 6 | |||
| 7 | 3. map reads to reference genome with bowtie2 |
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| 8 | #PE |
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| 9 | bowtie2 -p <number of alignment threads to launch> -x <path to Index filename prefix (minus trailing .X.bt2)> -1 <path to read 1 file> -2 <path to read 2 file> -S <path to output sam file> |
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| 10 | |||
| 11 | #SE |
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| 12 | bowtie2 -p <number of alignment threads to launch> -x <path to Index filename prefix (minus trailing .X.bt2)> -U <path to read 1 file> -S <path to output sam file> |