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.
a: Requires installation.
b: Duplicates calculated only for the first 200000 reads.
Table 1: Summary of the main characteristics of three SAM/BAM reporting tools.