bwa
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Bwa Command: Map Pair End Reads Mark Secondary Linux
Use for map pair end reads mark secondary linux with Bwa. Exact CLI syntax to map pair end reads mark secondary linux using Bwa.
When to use this: Use for map pair end reads mark secondary linux with Bwa.
Command Syntax
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 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>Live Command Builder
Final Command
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> Command Breakdown
-M- Command Option
- Tool-specific option used by this command invocation.
-t- Command Option
- Tool-specific option used by this command invocation.
FAQ
Purpose: Exact syntax to map pair end reads mark secondary 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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Suggest a correction, safer default, or version-specific note for this entry.
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 Linux 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 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> Autossh Command: Fork Autossh Background No Shell autossh -f -M <monitor_port> -N "<ssh_command>"