GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
nice tool. The usage examples are great, but there are non with an index parameter -i. This would be good, as I found it unusual to have to give the tool a .fasta and index.
Specifically, I was able to create a "SAM" file with binary elements in the header with the following command, supplying an index as a "reference" (should the FASTA parsing not check for FASTA format, it took in the index without complaining) and not supplying a fasta reference.
Hi,
nice tool. The usage examples are great, but there are non with an index parameter -i. This would be good, as I found it unusual to have to give the tool a .fasta and index.
Specifically, I was able to create a "SAM" file with binary elements in the header with the following command, supplying an index as a "reference" (should the FASTA parsing not check for FASTA format, it took in the index without complaining) and not supplying a fasta reference.
To be clear, this ran
graphmap -r lager2/rcug/seqres/HS/graphmap/hg19.fa.gmidx -d 37FB_nanopore.fastq -t 24 -o 37FB_nanopore_graphmap.sam
when I meant this
graphmap -r /lager2/rcug/seqres/HS/hg19.fa -i /lager2/rcug/seqres/HS/graphmap/hg19.fa.gmidx -d 37FB_nanopore.fastq -t 24 -o 37FB_nanopore_graphmap.sam
cheers, Colin