Difference between revisions of "Bwa"
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== Indexing == | == Indexing == | ||
| − | When bwa indexes a reference, it will use the whole filename and generate output index files with extensions added onto this name. | + | Before alignment, indexing the reference is necessary. When bwa indexes a reference, it will use the whole filename and generate output index files with extensions added onto this name. |
bwa index input_reference.fasta index_prefix | bwa index input_reference.fasta index_prefix | ||
| + | |||
| + | The index_prefix is then use for the actual alignment step which is as follows: | ||
| + | |||
| + | bwa mem index_prefix input_reads_pair_1.fastq input_reads_pair_2.fastq | ||
| + | |||
| + | In this case we have paired read-files. With single reads of course only one name would be required. | ||
Revision as of 14:23, 30 November 2016
Introduction
Heng Li's aligner.
Usage
As with samtools, bwa also went through some re-structuring, so that it has an old-style tw-step (aln and sam{s,p}e) usage, characterised by the following typical sequence of commands:
bwa index reference.fa bwa aln -I -t 8 reference.fa s_1.txt > out.sai bwa samse reference.fa out.sai s_1.txt > out.sam samtools view -bSu out.sam | samtools sort - out.sorted
And then a more modern usage which consists of just one step: bwa mem.
Indexing
Before alignment, indexing the reference is necessary. When bwa indexes a reference, it will use the whole filename and generate output index files with extensions added onto this name.
bwa index input_reference.fasta index_prefix
The index_prefix is then use for the actual alignment step which is as follows:
bwa mem index_prefix input_reads_pair_1.fastq input_reads_pair_2.fastq
In this case we have paired read-files. With single reads of course only one name would be required.
