Tools that output positions of matching kmers
Hello community!
I am trying to find a tool that takes sequencing reads as input and a genome. The tools breaks the reads into kmers and outputs the positions of the kmers within the genome for each read. As this is a standard step in almost every aligner I'm hoping I can find some tool that does it without having to write it by myself.
• 844 views
•
link
written
by
gil.hornung
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Is there any way to get the mismatch positions in the reads mapped by the Bowtie2 ?
written by Joyanta •
-
Tool to find double strand breaks
written by shelkmike
-
Aligning RNA-Seq short reads to a reference gene with semi global alignment
written by sr •
-
Getting GFF annotation from sequence coordinates.
written by jsporter
-
What should be the standard output of a mapper (not aligner)?
written by manetsus •
-
Tool for replacing variant-bases with reference in aligned reads, i.e anonymize bam files?
written by vegard nygaard
-
in silico enrichment
written by kamhamea •
-
Fasta Output Python Parsing
written by Richard
-
Counting Reads In Sam Format
written by Pdubois •
-
How To Convert Blast Results To Gff
written by Michael Barton •
But it is an intermediate step that most users are not interested in and it is used as a seed for initial matches. While someone else may know of a tool that does what you want, you could create a new read with each k-mer and have the aligner output the CIGAR match for those fake reads,
Curious as to why you want to do this?
Thanks, I thought there is a simpler and quicker option...