bwa
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Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
In bwa mem, when the insertion size cutoff is set as `[a, b]` (using the `-I` option), only the reads with the insertion size of `[a + 1, b +...
What does "Penalties for 5'-end and 3'-end clipping" mean in BWA-MEM? Does it refer to both soft and hard clipping? How can I prevent soft/hard clipping? I assumed that the...
What is the meaning of the -m option for bwa aln? It is only described at the command line as 'maximum entries in the queue', but I cannot find any...
As far as I know, bwa is released under GPLv3 while some files are under MIT License. On Apache2 branch, LICENSE.txt indicates it is under Apache 2.0 License. Can I...
-a means output all alignments for SE or unpaired PE, I find there is a bug two different ref, first is only a genome A, but second is thousands genomes...
Hi, When I wanted to run `bwa mem` with all alignment options `-a` and parallelization using `-t`, I find that the output only contains the best alignments. Even if I...
Dear bwa team, I am wondering whether mapping reads to a very short reference like the reference is only 1kb or so but reads are 150 bp. I do notice...
Good morining, Could you please prompt how to output a percentage and extract read pairs that have been concordantly aligned exactly 1 time form` sam` file, generated by `bwa mem`?...
Hello, just flagging that 'bwa.kit/run-gen-ref hs38DH' can not find the remote directory (see below error message). I have modified the url38 variable in the script url38="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz" and now it seems...
