bowtie-build builds a Bowtie index from a set of DNA sequences. bowtie-build outputs a set of 6 files with suffixes .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt. (If the total length of all the input sequences is greater than about 4 billion, then the index files will end in ebwtl instead of ebwt.) These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence files are no longer used by Bowtie once the index is built.
bowtie-build [options]* <reference_in> <ebwt_base>
Main arguments
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A comma-separated list of FASTA files containing the reference sequences to be aligned to, or, if |
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The basename of the index files to write. By default, |
Options
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The reference input files (specified as |
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The reference sequences are given on the command line. I.e. |
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Build a colorspace index, to be queried using |
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Disable the default behavior whereby |
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Use a packed (2-bits-per-nucleotide) representation for DNA strings. This saves memory but makes indexing 2-3 times slower. Default: off. This is configured automatically by default; use |
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The maximum number of suffixes allowed in a block. Allowing more suffixes per block makes indexing faster, but increases peak memory usage. Setting this option overrides any previous setting for |
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The maximum number of suffixes allowed in a block, expressed as a fraction of the length of the reference. Setting this option overrides any previous setting for |
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Use |
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Disable use of the difference-cover sample. Suffix sorting becomes quadratic-time in the worst case (where the worst case is an extremely repetitive reference). Default: off. |
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Do not build the |
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Build only the |
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To map alignments back to positions on the reference sequences, it's necessary to annotate ("mark") some or all of the Burrows-Wheeler rows with their corresponding location on the genome. |
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The ftab is the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first |
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Convert Ns in the reference sequence to As before building the index. By default, Ns are simply excluded from the index and |
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Endianness to use when serializing integers to the index file. Default: little-endian (recommended for Intel- and AMD-based architectures). |
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Use |
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Print usage information and quit. |
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Print version information and quit. |