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Table 1 Features comparison for various QC tools

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

  1. %FaQCs records a minimum of five bases of quality scores from both ends.
  2. *Uses a separate program/script to generate the result.
  3. #Module for Galaxy platform.
  4. $A separate web version is required.