minialign
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[IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long reads
Hello, I am attempting to use minialign to align subreads against a reference fasta. I am having two issues: Issue 1: I have generated the index using the following command...
Hi, I am comparing few nanopore aligners on ONT 1D and ONT 2D data, so I would like to verify if the general commands below are correct for those types...
Hello, I am trying to align some Pacbio reads using this command, after having built the index: ` minialign -l ref_index.mai SubPacbio.fq > out.sam` This returns ``` *** Error in...
It would be useful to implement calculation of the MD tag just like BWA does it. This allows to perform simple variant calling and estimating error rates from the BAM...
Hello Hajime, First of all, thanks for developing minialign! I was trying to map some simulated pacbio reads (from Pbsim) against both GRCH38 and hg19 references. Besides the default setting...
Greetings, I've noticed that alignments break over small deletions. Is there a way to control the size of deletion an alignment can contain? Thank you, Zev
Firstly, thanks for creating minialign! I noticed `-f` option have a large impact on the runtime and memory. Does `-f` have the same meaning as option -f in minimap? Also,...
Hi Hajime, Just curious, is minialign alignment accurate enough for Quiver genomic consensus corrections? Or do you have any other suggestions on sequence consensus corrections? Thanks, JW
This is a self issue report. Setting relatively large mismatch penalty respect to gap open penalty, such as `-a1 -b3 -p1 -q1`, sometimes results in broken CIGAR strings in the...
