Index

Symbols

--adapter-database adapterremoval3 command line option --adapter-fallback adapterremoval3 command line option --adapter-selection adapterremoval3 command line option --adapter-table adapterremoval3 command line option --adapter1 adapterremoval3 command line option --adapter2 adapterremoval3 command line option --barcode-mm adapterremoval3 command line option --barcode-mm-r1 adapterremoval3 command line option --barcode-mm-r2 adapterremoval3 command line option --barcode-orientation adapterremoval3 command line option --barcode-table adapterremoval3 command line option --compression-level adapterremoval3 command line option --convert-uracils adapterremoval3 command line option --demultiplex-only adapterremoval3 command line option --head adapterremoval3 command line option --help adapterremoval3 command line option --in-file1 adapterremoval3 command line option --in-file2 adapterremoval3 command line option --interleaved adapterremoval3 command line option --interleaved-input adapterremoval3 command line option --interleaved-output adapterremoval3 command line option --licenses adapterremoval3 command line option --log-colors adapterremoval3 command line option --log-level adapterremoval3 command line option --log-progress adapterremoval3 command line option --mask-degenerate-bases adapterremoval3 command line option --mate-separator adapterremoval3 command line option --max-length adapterremoval3 command line option --max-ns adapterremoval3 command line option --max-ns-fraction adapterremoval3 command line option --merge adapterremoval3 command line option --merge-quality-max adapterremoval3 command line option --merge-strategy adapterremoval3 command line option --merge-threshold adapterremoval3 command line option --min-complexity adapterremoval3 command line option --min-length adapterremoval3 command line option --min-mean-quality adapterremoval3 command line option --min-overlap adapterremoval3 command line option --mismatch-rate adapterremoval3 command line option --multiple-barcodes adapterremoval3 command line option --normalize-mate-separator adapterremoval3 command line option

--normalize-orientation adapterremoval3 command line option --out-discarded adapterremoval3 command line option --out-file1 adapterremoval3 command line option --out-file2 adapterremoval3 command line option --out-format adapterremoval3 command line option --out-html adapterremoval3 command line option --out-json adapterremoval3 command line option --out-merged adapterremoval3 command line option --out-prefix adapterremoval3 command line option --out-singleton adapterremoval3 command line option --out-unidentified1 adapterremoval3 command line option --out-unidentified2 adapterremoval3 command line option --post-trim-polyx adapterremoval3 command line option --post-trim3p adapterremoval3 command line option --post-trim5p adapterremoval3 command line option --pre-trim-polyx adapterremoval3 command line option --pre-trim3p adapterremoval3 command line option --prefix-merged adapterremoval3 command line option --prefix-read1 adapterremoval3 command line option --prefix-read2 adapterremoval3 command line option --preserve5p adapterremoval3 command line option --quality-format adapterremoval3 command line option --quality-trimming adapterremoval3 command line option --read-group adapterremoval3 command line option --report-duplication adapterremoval3 command line option --report-only adapterremoval3 command line option --report-sample-rate adapterremoval3 command line option --report-title adapterremoval3 command line option --shift adapterremoval3 command line option --simd adapterremoval3 command line option --stdout-format adapterremoval3 command line option --threads adapterremoval3 command line option --trim-min-quality adapterremoval3 command line option --trim-mott-rate adapterremoval3 command line option --trim-polyx-threshold adapterremoval3 command line option --trim-windows adapterremoval3 command line option --version adapterremoval3 command line option -h adapterremoval3 command line option -v adapterremoval3 command line option ...] adapterremoval3 command line option

A

adapterremoval3 command line option --adapter-database --adapter-fallback --adapter-selection --adapter-table --adapter1 --adapter2 --barcode-mm --barcode-mm-r1 --barcode-mm-r2 --barcode-orientation --barcode-table --compression-level --convert-uracils --demultiplex-only --head --help --in-file1 --in-file2 --interleaved --interleaved-input --interleaved-output --licenses --log-colors --log-level --log-progress --mask-degenerate-bases --mate-separator --max-length --max-ns --max-ns-fraction --merge --merge-quality-max --merge-strategy --merge-threshold --min-complexity --min-length --min-mean-quality --min-overlap --mismatch-rate --multiple-barcodes --normalize-mate-separator --normalize-orientation --out-discarded --out-file1 --out-file2 --out-format --out-html --out-json --out-merged --out-prefix --out-singleton --out-unidentified1 --out-unidentified2 --post-trim-polyx --post-trim3p --post-trim5p --pre-trim-polyx --pre-trim3p --prefix-merged --prefix-read1 --prefix-read2 --preserve5p --quality-format --quality-trimming --read-group --report-duplication --report-only --report-sample-rate --report-title --shift --simd --stdout-format --threads --trim-min-quality --trim-mott-rate --trim-polyx-threshold --trim-windows --version -h -v ...]