AdapterRemoval v2: rapid adapter trimming, identification, and read merging
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AdapterRemoval v2 : rapid adapter trimming, identification, and read merging. / Schubert, Mikkel; Lindgreen, Stinus; Orlando, Ludovic Antoine Alexandre.
I: BMC Research Notes, Bind 9, 88, 2016.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - AdapterRemoval v2
T2 - rapid adapter trimming, identification, and read merging
AU - Schubert, Mikkel
AU - Lindgreen, Stinus
AU - Orlando, Ludovic Antoine Alexandre
PY - 2016
Y1 - 2016
N2 - BACKGROUND: As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run.FINDINGS: We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support.CONCLUSIONS: We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.
AB - BACKGROUND: As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run.FINDINGS: We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support.CONCLUSIONS: We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.
U2 - 10.1186/s13104-016-1900-2
DO - 10.1186/s13104-016-1900-2
M3 - Journal article
C2 - 26868221
VL - 9
JO - BMC Research Notes
JF - BMC Research Notes
SN - 1756-0500
M1 - 88
ER -
ID: 160577276