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Questions tagged [read-mapping]

When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome).

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9 votes
2 answers
3k views

How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?

This is a problem I have to solve frequently, and I'd be interested in knowing what other methods people use to solve the same problem. About twice a year, I get asked to determine variants from ...
gringer's user avatar
  • 14.3k
15 votes
1 answer
5k views

Why is bwa-mem the standard algorithm when using bwa?

The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
terdon's user avatar
  • 10.2k
14 votes
2 answers
4k views

How does the BWA-MEM algorithm assign its mapping qualities?

Is there any resource (paper, blogpost, Github gist, etc.) describing the BWA-MEM algorithm for assigning mapping qualities? I vaguely remember that I have somewhere seen a formula for SE reads, which ...
Karel Břinda's user avatar
14 votes
4 answers
633 views

Library for computing BWT-based alignments

I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...
Daniel Standage's user avatar
11 votes
2 answers
3k views

Difference between BWA-backtrack and BWA-MEM

Many of my colleagues recommend I use BWA-MEM instead of regular old BWA. The problem is I don't understand why and reading the BWA man page doesn't seem to help the matter. What is the difference ...
David Ross's user avatar
7 votes
1 answer
104 views

How to interpret contig-alignment.psa produced by velvet

I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using ...
hhoomn's user avatar
  • 325
4 votes
1 answer
5k views

Hisat2 : which option should mention for strand specific library read

I was trying hisat2 I get confused by the strand options... The question has been already asked on github here but didn't get any satisfactory answer. I'm surprise how much this strand information ...
juke34's user avatar
  • 311
2 votes
3 answers
216 views

How to detect mismatch before mapping in RNA-Seq data

In the methods of this paper, the authors say: Reads were then filtered based on quality score in the UMI region. Any read with >1 low-quality base (phred <=10) were discarded. Reads with more ...
gc5's user avatar
  • 1,813
2 votes
0 answers
332 views

Merging/concatenating index files

I was wondering if any one has had success merging pre-generated reference index files for BWA, bowtie2 from multiple references? For a concrete example I have hg19 and a bunch of viral and ...
Bioathlete's user avatar
  • 2,574