From b6ea0b654cc8ebb6b3f121429a9051abb7eebc55 Mon Sep 17 00:00:00 2001 From: Maciej Michalczyk Date: Tue, 14 May 2024 15:57:17 +0200 Subject: [PATCH] bwa: add page (#12720) * bwa: add page --------- Co-authored-by: CleanMachine1 <78213164+CleanMachine1@users.noreply.github.com> Co-authored-by: K.B.Dharun Krishna Co-authored-by: Sebastiaan Speck <12570668+sebastiaanspeck@users.noreply.github.com> --- pages/linux/bwa.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 pages/linux/bwa.md diff --git a/pages/linux/bwa.md b/pages/linux/bwa.md new file mode 100644 index 0000000000000..e8896d5d255c0 --- /dev/null +++ b/pages/linux/bwa.md @@ -0,0 +1,25 @@ +# bwa + +> Burrows-Wheeler Alignment tool. +> Short, low-divergent DNA sequences mapper against a large reference genome, such as the human genome. +> More information: . + +- Index the reference genome: + +`bwa index {{path/to/reference.fa}}` + +- Map single-end reads (sequences) to indexed genome using 32 [t]hreads and compress the result to save space: + +`bwa mem -t 32 {{path/to/reference.fa}} {{path/to/read_single_end.fq.gz}} | gzip > {{path/to/alignment_single_end.sam.gz}}` + +- Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads and compress the result to save space: + +`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}}` + +- 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: + +`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}}` + +- 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: + +`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}}`