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Getting Started

Welcome to the brownieAligner wiki page!

brownieAligner is part of brownie software (see wiki page: https://github.com/jfostier/brownie/wiki).

brownieAligner aligns short Illumina reads to the de Bruijn graphs. To do this you need first builds the graph based on an input data (could be a reference genome for example)

brownie index [options] file1 [file2]...;

Then align your reads to the graph.

brownie align [options] [file_options] file1 [[file_options] file2]...

options:

-h    --help    display help page
options arg
-k      --kmersize            kmer size [default = 31]
-t      --threads             number of threads [default = available cores]
-e      --essa                sparseness factor of index structure [default = 1]
-nBB    --noBranchAndBound    do not use branch&Bound pruning
-nMM    --noMarkovModel       do not use Markov Model

file_options:

-o    output    aligned output read file name [default = inputfile.corr]