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GraphMap specifications

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Unique identifier OMICS_16089
Name GraphMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA/FASTQ
Biological technology Oxford Nanopore
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Version 0.4.1
Stability Stable
Maintained Yes

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Publication for GraphMap

GraphMap in publications

 (9)
PMCID: 5889714
PMID: 29431738
DOI: 10.1038/nbt.4060

[…] generated by ultra-long reads do not fit in the bam format specification, necessitating the use of sam or cram formats only (https://github.com/samtools/hts-specs/issues/40). instead, we used graphmap to align ultra-long reads to grch38, which took >25k cpu hours (). software optimized for long reads, including ngm-lr and minimap2 (ref. ), were faster: minimap2 took 60 cpu hours. […]

PMCID: 5740133
PMID: 29269933
DOI: 10.1038/s41598-017-18364-0

[…] 30% of the reads mapped to each organism (fig. ). across all eight flow cells, approximately 10% of reads (n = 8,960) did not match to either lambda, e. coli, or mouse by direct alignment using graphmap and surpirt (figs  and ). this was attributed to single-read error rates of 8–20% on the r7 version of flow cells used, as the use of a more sensitive aligner (blastn, e-value cutoff = 10−8) […]

PMCID: 5812507
PMID: 28961779
DOI: 10.1093/femsyr/fox074

[…] (https://metrichor.com/s/). the error rate of nanopore reads in the cen.pk113–7d frankfurt and delft was determined by aligning them to the final cen.pk113–7d assembly (see section below) using graphmap (sović et al.) and calculating mismatches based on the cigar strings of reads with a mapping quality of at least 1 and no more than 500 nt of soft/hard clipping on each end of the alignment […]

PMCID: 5543108
PMID: 28775309
DOI: 10.1038/s41598-017-07650-6

[…] it according to ont guidelines (https://github.com/nanoporetech/ont-assembly-polish). we first corrected nanopore-derived scaffolds with nanopore data using racon, based on alignments produced by graphmap version 0.3.0. ultimately racon sequence correction is performed by spoa, which is a partial order alignment algorithm that generates consensus sequences., subsequently, we used previously […]

PMCID: 5426553
PMID: 28503666
DOI: 10.21956/wellcomeopenres.12133.r21615

[…] ( ) to obtain the embedded fastq data. the respective fastq data were mapped to the reference human genome (grch38 primary assembly; genbank: gca_000001405.15) using graphmap (0.3.1; https://github.com/isovic/graphmap) ( ) with the --sensitive parameter enabled on a high performance computing cluster. high quality reads were mapped in 2d:17h using 14 threads. […]

GraphMap funding source(s)
Supported by the IMaGIN platform (project no. 102 101 0025), through a grant from the Science and Engineering Research Council, funding to the Genome Institute of Singapore from the Agency for Science, Technology and Research (A*STAR), Singapore, and funding from the Croatian Science Foundation (Project no. 7353—Algorithms for Genome Sequence Analysis).

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