├── .gitignore ├── .gitmodules ├── CMakeLists.txt ├── INSTALL ├── LICENSE ├── README.md ├── sam_stats ├── README ├── compare_two_sam_files.py ├── parse_sam.cpp ├── sam_stats.py └── test │ ├── read_cor.fa │ ├── read_uncor.fa │ ├── ref.fa │ └── run.sh ├── scripts ├── ascii_graph.py ├── jenkins │ ├── README │ ├── tool-bloocoo-build-debian7-64bits-gcc-4.7.sh │ ├── tool-bloocoo-build-macos-10.9.5-gcc-4.2.1.sh │ └── tool-bloocoo-release-debian.sh └── metaBloocoo ├── src ├── Bloocoo.cpp ├── Bloocoo.hpp ├── ReadWriter.cpp ├── ReadWriter.h └── main.cpp └── test ├── ERR039477.md5 ├── bloocoo_test.sh ├── bloocootest ├── Bloocoo ├── README ├── Rscripts │ ├── rec_pre_vs_err.R │ └── rec_pre_vs_threshold.R ├── build_bloocoo.sh ├── gener_alea ├── genomes │ └── ecoli.fasta ├── igrida │ ├── SOAPec │ │ ├── Corrector_AR │ │ ├── Corrector_HA │ │ ├── KmerFreq_AR │ │ └── KmerFreq_HA │ ├── coral │ ├── gener_alea │ ├── musket │ ├── mutareads │ └── racer ├── job.bash ├── jobs │ └── job1 │ │ ├── job.bash │ │ ├── output.freq.gz │ │ ├── output.freq.stat │ │ ├── read.lst │ │ ├── read.lst.QC.xls │ │ ├── reads.fasta.cor.pair.single.stat │ │ ├── reads.fasta.cor.stat │ │ ├── reads.fastq │ │ ├── reads.fastq.cor.pair.single.stat │ │ ├── reads.fastq.cor.stat │ │ ├── reads_bloocoo_corr_errs.tab │ │ ├── reads_corrected.fastq │ │ ├── test.py │ │ └── test_result │ │ ├── formatted_test_ecoli.tab │ │ └── test_ecoli.tab ├── libs │ ├── TestExec.py │ ├── TestExec.pyc │ ├── TestReadCorrection.py │ ├── TestReadCorrection.pyc │ ├── __init__.py │ └── __init__.pyc ├── main.py ├── musket ├── mutareads └── racer ├── datatest ├── err2del.fasta ├── err2delfin.fasta ├── err2ins.fasta ├── err2insfin.fasta ├── errclose.fasta ├── errdel.fasta ├── errdelfin.fasta ├── errins.fasta ├── errinsdeb.fasta ├── errinsfin.fasta ├── errleft.fasta ├── errm.fasta ├── errright.fasta ├── true2errdelfin ├── true_del2 ├── true_err2insfin ├── true_errdel1 ├── true_errdelfin ├── true_errins1 ├── true_errins2 ├── true_errinsfin ├── 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