From: Rapid evaluation and quality control of next generation sequencing data with FaQCs
Features\Tools | FaQCs | FastQC v0.10.0 | FASTX-Toolkits v0.0.13 | PRINSEQ lite v0.20.4 | SolexaQA v2.2 |
---|---|---|---|---|---|
3’ end quality trimming | Yes | No | Yes | Yes | Yes |
5’ end quality trimming | Yes | No | No | Yes | Yes |
Cross quality spike trimming % | Yes | No | No | No | No |
Adapter/Primer trimming | Yes | No | Yes | No | No |
PhiX filtering | Yes | No | No | No | No |
Low complexity filtering | Yes | No | Yes | Yes | No |
“N” base filtering | Yes | No | Yes | Yes | No |
Length filtering | Yes | No | Yes | Yes | Yes* |
Sequence duplication filtering | No | No | Yes | Yes | No |
Kmer content/rarefaction | Yes | Yes | No | No | No |
Graphic quality report output | Yes | Yes | Yes* | Yes* | Yes |
GC (nucleotide) content distribution | Yes | Yes | Yes | Yes | No |
Fastq format conversion | Yes | No | No | No | No |
Multiple fastq inputs | Yes | Yes | No | No | Yes |
Process paired-end data | Yes | No | No | Yes | Yes* |
Accept fastq variants format | Yes | Yes | No | Yes | Yes |
Support compressed gzip input data | Yes | Yes | No | Yes | No |
Multi-threaded | Yes | Yes | No | No | No |
Stand-alone tool/Command line | Yes | Yes | Yes | Yes | Yes |
Web-interface | Yes # | Yes | Yes # | Yes $ | No |