de Bruijn Workflow using Integral information of Short paired-End reads

Work in progress -- so far, this assembler works well with > 100X of 2*250 bp Illumina reads (recommended fragment library size ~500-600 bp).

(requires GCC>=4.9, GIT, MAKE and CMAKE3).

git clone https://github.com/Malfoy/BWISE --depth 1

cd BWISE

./install_git.sh

will download and compile the latest version of the needeed programs Possible compilation options:

-p absolute path of folder to put the binaries

-t use multiple threads for compilation (default is 8)

You can test your installation as follows:

./test_install.sh

Will skip Bcalm compilation and download the release binary instead.

This instalation is faster and do not need cmake but large Kmer size (> 101) can not be used.

git clone https://github.com/Malfoy/BWISE --depth 1

cd BWISE

./install_git.sh -f

./test_install.sh

(requires GCC>=4.9, GIT, MAKE and CMAKE3).

Get the latest release:

wget https://github.com/Malfoy/BWISE/releases/download/V0.1/Bwise01.tgz

tar -xvf Bwise01.tgz

cd BWISE

./install_src.sh

will compile the programs of the downloaded release Possible compilation options:

-f absolute path of folder to put the binaries

-t use multiple threads for compilation (default is 8)

./update.sh will update the components of Bwise

Possible compilation options:

-f absolute path of folder to put the binaries

-t use multiple threads for compilation (default is 8)

You can test your installation as follows:

./test.sh

python3 Bwise.py -x examplePairedReads.fa -o workingFolder

Options and default values:

-h, --help show this help message and exit

-x PAIRED_READFILE input fasta/fastq (fa, fa.gz, fq or fq.gz) paired-end read files. Only one input file of this type can be used: if you have for instance two paired-end librairies (e.g. libA and libB), first interleave the forward and reverse reads for each library. This may be done using the provided script src/two_fastq_to_interleaved_fasta.py:

python src/two_fastq_to_interleaved_fasta.py libA_1.fq libA_2.fq > interleavedlibA.fa

and

python src/two_fastq_to_interleaved_fasta.py libB_1.fq libB_2.fq > interleavedlibB.fa

and then concatenate the two resulting files in order to generate the PAIRED_READFILE input fasta):

cat interleavedlibA.fa interleavedlibB.fa > interleavedlibsA+B.fa

-u SINGLE_READFILE input fasta/fastq (fa, fa.gz, fq or fq.gz) single-read files. Only one input file of this type can be used: if you have several single-read librairies, concatenate them to generate the SINGLE_READFILE input fasta).

-s KMER_SOLIDITY an integer, k-mers present strictly less than this number of times in the dataset will be discarded (default 2)

-S KMER_COVERAGE an integer, minimal unitig coverage for first cleaning (default 5)

-p SR_SOLIDITY an integer, super-reads present strictly less than this number of times will be discarded (default 3)

-P SR_COVERAGE an integer X, unitigs with less than X reads mapped is filtred (default 3)

-k K_MIN an integer, smallest k-mer size (default 63)

-K K_MAX an integer, largest k-mer size (default 63). Advice: put a -K near slightly below your read size (241 for 250 bp reads for example)

-e MAPPING_EFFORT number of anchors to test for mapping (default max)

-a ANCHOR_SIZE size of the anchors (default 31)

-m MISSMATCH_ALLOWED number of missmatchs allowed in mapping (default 0)

-t NB_CORES number of cores used (default 1)

-o OUT_DIR path to store the results (default = current directory)

--version show program's version number and exit