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Table 1 Summary of existing removal tools listed together with some of their relevant features

From: Removing duplicate reads using graphics processing units

Tool Strategy Libraries Platform Type
Picard MarkDuplicates alignment-based single- and paired-end Illumina and 454 nearly-identical
samtools rmdup alignment-based single- and paired-end Illumina and 454 nearly-identical
SEAL alignment-based paired-end Illumina nearly-identical
FastX-Toolkit Collapser alignment-free single-end Illumina and 454 identical
FastUniq alignment-free paired-end Illumina and 454 identical
Fulcrum alignment-free single- and paired-end Illumina and 454 nearly-identical
CD-HIT-454 alignment-free single- and paired-end 454 nearly-identical
CD-HIT-DUP alignment-free single- and paired-end Illumina nearly-identical
  1. The second column indicates the implemented strategy. The third column reports whether the corresponding tool support single- and/or paired-end read libraries. The fourth column reports the sequencing platforms supported. The fifth column reports whether the corresponding tool is able to remove only identical or nearly-identical duplicates