Feature |
SAM-Profiler |
SamStat |
FastQC |
Operative System |
L/W/M |
L |
L/W/M |
Graphical UI |
Yes |
No |
Yes |
Programming Language |
C# |
C |
Java |
External Dependencies |
.Net/Mono Runtime |
Noa |
Java Runtime |
Input |
SAM/BAM |
SAM/BAM |
SAM/BAM |
Batch Input |
Yes |
Yes |
No |
Interactive Graphical Output |
Yes |
No |
No |
Parallel programming |
Yes |
No |
Yes |
Read Quality |
Yes |
Yes |
Yes |
Mapping Quality |
Yes |
Yes |
No |
Per-Read Read Quality |
Yes |
No |
No |
Per-Base Read Quality |
Yes |
No |
Yes |
Per-Chromosome Read Quality |
Yes |
No |
No |
Nucleotides Overrepresentation |
No |
Yes |
Yes |
Duplicates |
Yes |
No |
Yesb |
Per-Chromosome Duplicates |
Yes |
No |
No |
Exonic/Intronic/Intergenic Coverage |
Yes |
No |
No |
Exonic Fold-Coverage |
Yes |
No |
No |
Fragment Size Distribution |
Yes |
No |
No |
Perfectly/Imperfectly Mapped Reads |
Yes |
No |
No |
Properly/Improperly Pairs |
Yes |
No |
No |
M/U and U/U Pairs |
Yes |
No |
No |
Improperly Mapped Reads Analysis |
Yes |
No |
No |
Mismatch Distribution |
Yes |
Yes |
No |
Per-Read CG Distribution |
Yes |
No |
Yes |
A,C,T,G,N Distribution |
Yes |
Yes |
Yes |
L/W/M: Linux/Windows/MacOS.