Skip to main content

Table 1 A feature comparison of AfterQC with existing tools. From the table we can find that AfterQC is versatile on common quality control and data filtering tasks, and offers novel features not implemented by other tools before

From: AfterQC: automatic filtering, trimming, error removing and quality control for fastq data

  FastQC Trimmomatic Cutadapt AfterQC
Quality Control Rich functions Few function Few function Rich functions
Auto Trimming None Read by read Read by read Global Trimming
Cutting adapter None Single-end/pair-end Single-end/pair-end Pair-end only
PolyX filtering None None None Supported
Figure plotting Static Static Static Interactive
Overlap analysis None Cutting adapter only None Supported with error correction
Sequence error profiling None None None Supported
Bubble detection None None None Supported
Programming Language Java Java Python Python, C
Speed Fast Fast Fast Fast only for single-end