mirror of https://github.com/CrimsonTome/tldr.git
26 lines
1.4 KiB
Markdown
26 lines
1.4 KiB
Markdown
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# bwa
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> Burrows-Wheeler Alignment tool.
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> Short, low-divergent DNA sequences mapper against a large reference genome, such as the human genome.
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> More information: <https://github.com/lh3/bwa>.
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- Index the reference genome:
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`bwa index {{path/to/reference.fa}}`
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- Map single-end reads (sequences) to indexed genome using 32 [t]hreads and compress the result to save space:
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`bwa mem -t 32 {{path/to/reference.fa}} {{path/to/read_single_end.fq.gz}} | gzip > {{path/to/alignment_single_end.sam.gz}}`
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- Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads and compress the result to save space:
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`bwa mem -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
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- Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads with [M]arking shorter split hits as secondary for output SAM file compatibility in Picard software and compress the result:
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`bwa mem -M -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
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- Map pair-end reads (sequences) to indexed genome using 32 [t]hreads with FASTA/Q [C]omments (e.g. BC:Z:CGTAC) appending to a compressed result:
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`bwa mem -C -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
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