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Bwa Command: Map Pair End Reads Linux
Use for map pair end reads linux with Bwa. Exact CLI syntax to map pair end reads linux using Bwa.
When to use this: Use for map pair end reads linux with Bwa.
Command Syntax
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>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>Command Breakdown
-t- Command Option
- Tool-specific option used by this command invocation.
FAQ
Purpose: Exact syntax to map pair end reads linux using Bwa.
Test path: Replace placeholders and run destructive commands in a disposable workspace first.
Flag behavior: Tool version, platform, and shell can change behavior.
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Related Operations
Bwa Command: Index Reference Genome Linux
bwa index <path/to/reference.fa> Bwa Command: Map Pair End Reads Append Comments Linux 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> Bwa Command: Map Pair End Reads Mark Secondary Linux 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> Bwa Command: Map Single End Reads Linux bwa mem -t 32 <path/to/reference.fa> <path/to/read_single_end.fq.gz> | gzip > <path/to/alignment_single_end.sam.gz> Jmeter Command: Run Test Plan Nongui jmeter -n -t <path/to/file.jmx>