AdapterRemoval: easy cleaning of next-generation sequencing reads

BMC Research Notes

Table 1 Comparison of various tools for trimming adapters

The table summarizes the features of different programs that are aimed at removing adapter sequences from next-generation sequencing reads. For each method, the table shows if it is able to i) identify adapters in the 5’ end of reads, ii) identify adapters in the 3’ end of reads, iii) process single-end reads, iv) process paired-end reads, v) collapse overlapping pairs, vi) search for multiple different adapters, vii) trim subsequences of Ns, viii) trim low-quality nucleotides, ix) sort multiplexed reads based on barcodes. The last feature is not as such related to adapter trimming but since it occurs often in these programs it is included. The table also lists references for each program. Notes: 1) If chosen, reads with one or more Ns are discarded (i.e. Ns are not trimmed). 2) If chosen, low-quality reads are discarded (i.e. low-quality nucleotides are not trimmed). 3) Discards remaining read if the other read in a pair is removed due to trimming. 4) The aim of this program is slightly different as it compares the reads to a library of sequences and checks for significant overlap.

ISSN: 1756-0500