bwa
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lh3
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Pre-processing tools like _AfterQC_ and _fastp_ can perform adapter clipping leaving both reads in a pair identical. This leads them to be mapped at the same location by `aln`, leading...
I was benchmarking `bwa` with various EC2 configurations to decide which to choose for our Batch jobs. We blindly used `Alpine` as a base image which uses different GCC compiler....
I've recently suffered a lot from indexing a customized human genome (mask certain regions). I found several issues shown as below: 1st:  But I use ls -lh and confirmed...
I want to run bwa_mem, but I always get this error. I can't run it. The index is correct. What's the situation? Thank you [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process]...
I have noticed that insert sizes from BWA-MEM seem to start high at the beginning of a chromosome, and drop down towards the end. This isn't really an issue (feel...
HI Dr. Li, I want to adjust bwa single-end mapping for perfect matched alignment, i.e., ignore writing supplementary gapped or mismatched alignment to SAM. Do you have any directions on...
When processing Illumina >1.8 reads, the reads are marked as filtered out or not. This is known as chastity filter. Usually, those reads are taken away and not used, but...
` sort -r ucsc.hg19.genome.fa -o /a23916.sorted.bam -t 24 --sam2bam -i - ` [M::bwa_idx_load_from_disk] read 0 ALT contigs [bwt_resample_sa] Failed to allocate 6191354832 bytes at bwt.c line 809: Cannot allocate memory...
I am trying to install bwa at a Linux Cluster and the make command fail at this point ``` gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o...
