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
- BamView.
- Pros: Good paired-end support (similar to Gap5)
- Cons: very limited features; unable to show each base; UI can be improved.
- Gap5,
the successor of the famous Gap4.
- Pros: support editing, padding and quick overview.
- Cons: difficult to install
[reference].
- GenomeView. I
have not tried it yet and thus not shown in the table below.
- Integrative Genomics
Viewer (IGV), a versatile viewer with the support of the
SAM/BAM format recently.
- Pros: support annotation tracks; load data on the IGV server;
fast viewing over network
- Cons: may have problem when network is not available (version
1.3 beta)
- MapView
[PMID: 19369497],
a user friendly alignment viewer in active development.
- Pros: user friendly
- Cons: short read only; no indel; limited compression
- Maqview,
the MAQ only alignment viewer.
- Pros: user friendly.
- Cons: no indel; no PE; MAQ alignment format only; windows
version is ported by the 3rd party
- SAMtools
tview
[PMID: 19505943],
a small text alignment viewer.
- Pros: fast across networks; open alignments on FTP/HTTP.
- Cons: less fancy; limited zooming (via terminal); no PE
support.
- Tablet.
- Pros: elegant and responsive interface; supporting many
formats
- Cons: Limited features (e.g. no quality display, no PE);
annotation display can be improved; too strict on the BAM format.
- Others. I have
tried Gambit and
MagicViewer,
but they either crashed or failed to display the alignment. My
example alignment file is a mix of short reads and long Sanger reads
in a 5Mbp region extracted from two whole human genome
alignments. It may contain minor errors (e.g. lack of mates), but a
good viewer should be robust to them.
| Features | BamView | Gap5 | IGV | MapView | Maqview | SAMtools | Tablet |
|---|
| Native Format | SAM | Gap5 | SAM | MVF | MAQ | SAM | SAM+ |
|---|
| User Interface | Java | X11/tk | Java | .NET | OpenGL | Curses | Java |
|---|
| Unix-like | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
|---|
| Windows | Yes | No | Yes | Yes | 3rd-party | Yes | Yes |
|---|
| Zoom | Partial | Yes | Yes | Yes | Yes | Via terminal | Yes |
|---|
| Display mapQ | No | Yes | Partial | No | Yes | 4 colors | No |
|---|
| Gradient baseQ | No | Yes | Yes | No | Yes | 4 colors | No |
|---|
| Paired-end | Yes | Yes | Partial | Yes | No | Orphan only | No |
|---|
| Long reads | Yes | Yes | Yes | No | No | Yes | Yes |
|---|
| Deletion | No | Yes | Yes | No | No | Yes | Yes |
|---|
| Insertion | No | Yes | Partial | No | No | Yes | No |
|---|
| Padding | No | Yes | No | No | No | No | No |
|---|
| Editing | No | Yes | No | No | No | No | No |
|---|
| Annotation Track | Limited | No | Yes | No | No | No | Limited |
|---|
| Multiple tracks | No | No | Yes | No | Yes | No | No |
|---|
| Open remote | No | No | Yes | No | No | Yes | No |
|---|