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
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.