Introduction

Here I only focus on the software packages that are capable of viewing the entire 40X alignment against the human genome. Gap4, Consed, Hawkeye and EagleView are all good assembly viewers, but it is impractical to use them on huge alignments/assemblies.


Software


FeaturesBamViewGap5IGVMapViewMaqviewSAMtoolsTablet
Native FormatSAMGap5SAMMVFMAQSAMSAM+
User InterfaceJavaX11/tkJava.NETOpenGLCursesJava
Unix-likeYesYesYesYesYesYesYes
WindowsYesNoYesYes3rd-partyYesYes
ZoomPartialYesYesYesYesVia terminalYes
Display mapQNoYesPartialNoYes4 colorsNo
Gradient baseQNoYesYesNoYes4 colorsNo
Paired-endYesYesPartialYesNoOrphan onlyNo
Long readsYesYesYesNoNoYesYes
DeletionNoYesYesNoNoYesYes
InsertionNoYesPartialNoNoYesNo
PaddingNoYesNoNoNoNoNo
EditingNoYesNoNoNoNoNo
Annotation TrackLimitedNoYesNoNoNoLimited
Multiple tracksNoNoYesNoYesNoNo
Open remoteNoNoYesNoNoYesNo