The following instructions assume Linux or OS X. For more information, including Windows instructions, refer to the SeqAn getting started tutorial.

A modern C++11 compiler with OpenMP 3.0 extensions is required to build Yara. If unsure, use GNU G++ 4.9 or newer.

• Git.
• CMake 3.2 or newer.
• G++ 4.9 or newer.

Misc sources downloaded by executing:

$git clone https://github.com/svnbgnk/misc.git

Create a build project by executing CMake as follows:

$ mkdir misc-build
$ cd misc-build
$ cmake ../misc

Invoke make as follows:

$ make

Count alternative Alignments of a single Occurrence when search with up 3 errors with my Version of the OSS

$ testOSSAlignments -l 100 -mv -e 3

MapMap setup (requires 6-7 GB of RAM)

$ git clone --recurse-submodules https://github.com/svnbgnk/dream_yara.git
$ git checkout oss
$ cd dream_yara/include/seqan/
$ git remote add upstream https://github.com/svnbgnk/seqan.git
$ git checkout upstream/mappa
$ cd ../../..
$ mkdir mapmap-build
$ cd mapmap-build
$ cmake ../dream_yara
$ make all

Acquiring hg38.fa

$ DATA/reference
$ wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
$ gunzip hg38.fa.gz
$ mkdir bin
$ cp hg38.fa bin/0.fa

Building the Index (requires 200GB of secondary memory)

$ dream_yara_indexer --threads 8 --output-prefix DATA/hg38_N_index/ DATA/reference/bin/*.fa -td /srv/public/svnbngk/tmp/

Computing sequence mappability and bit vectors with TH = 10

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 3 -T 10 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability10E3

All mapping with up to 3 errors

$ dream_yara_mapper DATA/hg38_N_index/ DATA/reads/illumina/illumina_1.fa -t 1 -b 1 -ft none -e 3 -s 3 -o result.sam -vv

Stratified all-mapping with strata 2 and 3 errors

$ dream_yara_mapper DATA/hg38_N_index/ DATA/reads/illumina/illumina_1.fa -t 1 -b 1 -ft none -e 3 -s 3 -o result.sam -vv

Mapping with sequence mappability up to 3 errors

$ dream_yara_mapper DATA/hg38_N_index/ DATA/reads/illumina/illumina_1.fa -t 1 -b 1 -ft none -e 3 -s 3 -m DATA/hg38_N_index/mappability10E3/ -o result.sam -vv

Default OSS

$ testOSSAlignments -l 100 -e 1
$ testOSSAlignments -l 100 -e 2
$ testOSSAlignments -l 100 -e 3
$ testOSSAlignments -l 100 -e 4

With 1 read error

$ testOSSAlignments -l 100 -e 4 -em -m 1

Simulating on MapMap OSS

$ testOSSAlignments -l 100 -mv -e 1
$ testOSSAlignments -l 100 -mv -e 2
$ testOSSAlignments -l 100 -mv -e 3
$ testOSSAlignments -l 100 -mv -e 4

With 1 read error

$ testOSSAlignments -l 100 -mv -e 3 -em -m 1

Computation of Sequence Mappability:

T = 5

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 3 -T 5 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability5E3

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 2 -T 5 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability5E2

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 1 -T 5 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability5E1

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 3 -T 5 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability5H3

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 2 -T 5 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability5H2

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 1 -T 5 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability5H1

T = 10

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 3 -T 10 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability10E3

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 2 -T 10 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability10E2

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 1 -T 10 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability10E1

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 3 -T 10 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability10H3

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 2 -T 10 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability10H2

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 1 -T 10 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability10H1

T = 100

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 3 -T 100 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability100E3

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 2 -T 100 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability100E2

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 2 -T 100 -s 0 -t 20 -o 35 -v -i -O DATA/hg38_N_index/mappability100E1

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 3 -T 100 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability100H3

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 2 -T 100 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability100H2

$ dream_yara_mappability DATA/hg38_N_index/ -b 1 -K 100 -E 1 -T 100 -s 0 -t 20 -o 35 -v -O DATA/hg38_N_index/mappability100H1

Using bashscripts in ./bashscripts and reads in ./reads

$ benchmark_v2.sh master.log DATA/hg38_N_index/ DATA/reads/illumina/illumina_1.fa

$ benchmark_hamming.sh masterHamming.log DATA/hg38_N_index/ DATA/reads/illumina/illumina_1.fa

$ benchmark_f2.sh map5.log srv/public/svnbngk/Data/hg38_N_index/ DATA/reads/illumina/illumina_1.fa DATA/hg38_N_index/ mappability5

$ benchmark_f2.sh map10.log srv/public/svnbngk/Data/hg38_N_index/ DATA/reads/illumina/illumina_1.fa DATA/hg38_N_index/ mappability10

$ benchmark_f2.sh map100.log srv/public/svnbngk/Data/hg38_N_index/ DATA/reads/illumina/illumina_1.fa DATA/hg38_N_index/ mappability100

Benchmarking Dream-Yara on a bidirectional index (based on EPR dictionaries) use flag -of

Benchmarking Dream-Yara with -ft none on a unidirectional Index

$ git checkout yaraben

To use my fix for mapping without an filter.