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CoLoRMap specifications


Unique identifier OMICS_12705
Name CoLoRMap
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Similar to most hybrid methods for error correction, CoLoRMap gets as input two sets of reads namely short reads and long reads from the same donor.
Biological technology Pacific Biosciences, Oxford Nanopore
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
BWA, SAMtools, Minia
Maintained Yes


No version available



  • person_outline Ehsan Haghshenas <>

Publication for CoLoRMap

CoLoRMap citations


Iron specific Signal Separation from within Heavy Metal Stained Biological Samples Using X Ray Microtomography with Polychromatic Source and Energy Integrating Detectors

PMCID: 5953933
PMID: 29765060
DOI: 10.1038/s41598-018-25099-z

[…] be uranium. a calibration based on the known material concentration was performed to scale either the “high” or “low” image, obtaining the iron material density image [mgfe/cc] shown in fig.  in red colormap, and uranium material density image [mgu/cc] shown in fig.  in green colormap., material analysis can also be done by way of material basis decomposition,,, whereby the absorption […]


Integrated fMRI Preprocessing Framework Using Extended Kalman Filter for Estimation of Slice Wise Motion

PMCID: 5932184
PMID: 29755312
DOI: 10.3389/fnins.2018.00268

[…] surfaces, optionally inflated, of both hemispheres as well as subcortical structures represented as voxel cloud enclosed in transparent boundary surfaces colored by freesurfer atlas colors. the colormap represent the values of the displayed data overlaid on curvature grayscale values (as illustrated in figure with t-values), the sizes of the subcortical voxels also vary with these values […]


Quantifying the three dimensional facial morphology of the laboratory rat with a focus on the vibrissae

PMCID: 5886528
PMID: 29621356
DOI: 10.1371/journal.pone.0194981

[…] uniform dispersion of actual vs. predicted values about the identity line, reflecting correct model choice. finally, the quadratic variation of for φbp across the whisker array is shown in as a colormap., we next examined the relationship between rbp and the basepoint parameters θbp and φbp. shows rbp to be quadratically related to θbp and linearly related to φbp: […]


Multi Target Tracking of Human Spermatozoa in Phase Contrast Microscopy Image Sequences using a Hybrid Dynamic Bayesian Network

PMCID: 5864867
PMID: 29568044
DOI: 10.1038/s41598-018-23435-x

[…] a video camera (basler vision tecnologie a312fc). two non-consecutive, randomly selected microscopic fields per sample were scanned. the captured image resolution was 768 by 576 pixels, and the colormap was 8-bit grayscale. the recorded samples were varied in terms of spermatozoa cell count, the existence of other cells (e.g., debris or blood cells), and noise level. here, the spermatozoa […]


Widefield standing wave microscopy of red blood cell membrane morphology with high temporal resolution

PMCID: 5905920
PMID: 29675316
DOI: 10.1364/BOE.9.001745

[…] for all remaining data points were then determined using the cubic interpolation method. by extracting all the intensity values from the antinodal planes in the sw red blood cell images, a custom colormap is created and was assigned to the correct coordinate. the final 3d reconstruction is created using the scatter3 and surf matlab functions and was stored as a .tiff stack which was converted […]


A comparative assessment of inhomogeneity and finite patient dimension effects in 60Co and 192Ir high dose rate brachytherapy

PMCID: 5881600
PMID: 29619059
DOI: 10.5114/jcb.2018.74327

[…] the high-dose volume close to the sources is discarded from the comparison., presents tg-43 and mc dosimetry results for an indicative breast case, in the form of isodose lines superimposed on a colormap of pixel-by-pixel percentage dose differences relative to mc, for the 60co and the 192ir treatment plans, on axial, sagittal, and coronal planes. target and oars contours are also delineated […]

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CoLoRMap institution(s)
School of Computing Sciences, Simon Fraser University, Burnaby, BC, Canada; MADD-Gen Graduate Program, Simon Fraser University, Burnaby, BC, Canada; Vancouver Prostate Centre, Vancouver, BC, Canada; School of Informatics and Computing, Indiana University, Bloomington, IN, USA; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
CoLoRMap funding source(s)
NSERC CREATE fellowship (139277); an NSERC Discovery frontiers grant on ‘Cancer Genome Collaboratory’; an NSERC Discovery Grant (249834)

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