Questions tagged [alignment]

These questions are about sequence alignment.

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2
votes
3answers
1k views

How does blastn sort output?

I used blastn to search one a genome database for the sequences in a file. ...
5
votes
2answers
196 views

How to estimate whether a long-read is meaningful sequence?

The setup Imagine that I work on an organism without a reference genome, and that the closest reference genome I can get is quite diverged. E.g. ~10% diverged in terms of SNVs when measured with ...
8
votes
1answer
388 views

Aligning many long sequences

I'm faced with having to align many (some 100s) bacterial genomes, where the genome length is in the millions. Obviously, this is beyond normal alignment techniques and it's unclear to me what the ...
8
votes
2answers
538 views

Building STAR Genome Index for nanopore RNA sequencing

I am aligning a dataset of 1,000,000 reads oh human mRNA sequenced on Oxford Nanopore Technologies' MinION, and would like to use the STAR aligner, using the parameters recommended by Pacific ...
16
votes
2answers
8k views

Obtaining uniquely mapped reads from BWA mem alignment

This is based on a question from betsy.s.collins on BioStars. The original post can be found here. Does anyone have any suggestions for other tags or filtering steps on BWA-generated BAM files that ...
12
votes
4answers
511 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. ...
12
votes
1answer
3k views

What is the difference between samtools, bamtools, picard, sambamba and biobambam?

After some google searches, I found multiple tools with overlapping functionality for viewing, merging, pileuping, etc. I have not got time to try these tools, so will just see if anyone already know ...
14
votes
1answer
3k 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 ...
6
votes
2answers
244 views

How can I output an identity matrix in progressiveMauve?

I'm just getting started with the Mauve aligner and I'm finding the documentation a bit lacking. I'm using the progressiveMauve tool from the command line and would ...
7
votes
1answer
569 views

The effects of incomplete bisulfite conversion upon mapping efficiency

This question has also been posted on Biostars I have sequenced numerous multiplexed pools of BS amplicon-seq libraries derived from human samples on a MiSeq over the past few weeks. I have been ...
15
votes
2answers
7k views

Merge hundreds of small BAM files into a single BAM file

I am working with over a million (long) reads, and aligning them to a large genome. I am considering running my alignment jobs in parallel, distributing horizontally across hundreds of nodes rather ...
7
votes
2answers
503 views

Understanding the significance of BLAT score calculations for read fragment alignment

I'm attempting to reconstruct the read fragments that form a hit to a target, excluding/skipping gaps. BLAST's outfmt 6, and alternatives such as Diamond's ...
13
votes
1answer
205 views

Compare alignment quality of multiple sequencing runs aligned against the same reference genome

I have run Oxford Nanopore Technologies' MinION sequencing on the same DNA sample using three flowcells, each aligned against the same reference genome (E.coli K12 MG1655) using both BWA MEM and ...
11
votes
2answers
2k 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 ...

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