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    - [RsphF: quorum](#rsphf-quorum)
    - [RsphF: down sampling](#rsphf-down-sampling)
    - [RsphF: k-unitigs and anchors (sampled)](#rsphf-k-unitigs-and-anchors-sampled)
    - [RsphF: merge anchors](#rsphf-merge-anchors)
- [*Vibrio cholerae* CP1032(5) Full](#vibrio-cholerae-cp10325-full)
    - [VchoF: download](#vchof-download)
    - [VchoF: combinations of different quality values and read lengths](#vchof-combinations-of-different-quality-values-and-read-lengths)
    - [VchoF: quorum](#vchof-quorum)
    - [VchoF: down sampling](#vchof-down-sampling)
    - [VchoF: k-unitigs and anchors (sampled)](#vchof-k-unitigs-and-anchors-sampled)
    - [VchoF: merge anchors](#vchof-merge-anchors)


# *Bacillus cereus* ATCC 10987

## Bcer: download

* Reference genome

    * Strain: Bacillus cereus ATCC 10987
    * Taxid: [222523](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=222523)
    * RefSeq assembly accession:
      [GCF_000008005.1](ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/005/GCF_000008005.1_ASM800v1/GCF_000008005.1_ASM800v1_assembly_report.txt)
    * Proportion of paralogs (> 1000 bp): 0.0797

```bash
BASE_NAME=Bcer
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 1_genome
cd 1_genome

aria2c -x 9 -s 3 -c ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/005/GCF_000008005.1_ASM800v1/GCF_000008005.1_ASM800v1_genomic.fna.gz

TAB=$'\t'
cat <<EOF > replace.tsv
NC_003909.8${TAB}1
NC_005707.1${TAB}pBc10987
EOF

faops replace GCF_000008005.1_ASM800v1_genomic.fna.gz replace.tsv genome.fa

cp ~/data/anchr/paralogs/gage/Results/Bcer/Bcer.multi.fas paralogs.fas

```

* Illumina

    Download from GAGE-B site.

```bash
BASE_NAME=Bcer
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 2_illumina
cd 2_illumina

aria2c -x 9 -s 3 -c http://ccb.jhu.edu/gage_b/datasets/B_cereus_MiSeq.tar.gz

# NOT gzipped tar
tar xvf B_cereus_MiSeq.tar.gz raw/frag_1__cov100x.fastq
tar xvf B_cereus_MiSeq.tar.gz raw/frag_2__cov100x.fastq

cat raw/frag_1__cov100x.fastq \
    | pigz -p 8 -c \
    > R1.fq.gz
cat raw/frag_2__cov100x.fastq \
    | pigz -p 8 -c \
    > R2.fq.gz

rm -fr raw
```

* GAGE-B assemblies

```bash
BASE_NAME=Bcer
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 8_competitor
cd 8_competitor

aria2c -x 9 -s 3 -c http://ccb.jhu.edu/gage_b/genomeAssemblies/B_cereus_MiSeq.tar.gz

tar xvfz B_cereus_MiSeq.tar.gz abyss_ctg.fasta
tar xvfz B_cereus_MiSeq.tar.gz cabog_ctg.fasta
tar xvfz B_cereus_MiSeq.tar.gz mira_ctg.fasta
tar xvfz B_cereus_MiSeq.tar.gz msrca_ctg.fasta
tar xvfz B_cereus_MiSeq.tar.gz sga_ctg.fasta
tar xvfz B_cereus_MiSeq.tar.gz soap_ctg.fasta
tar xvfz B_cereus_MiSeq.tar.gz spades_ctg.fasta
tar xvfz B_cereus_MiSeq.tar.gz velvet_ctg.fasta

```

* FastQC

```bash
BASE_NAME=Bcer
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 2_illumina/fastqc
cd 2_illumina/fastqc

fastqc -t 16 \
    ../R1.fq.gz ../R2.fq.gz \
    -o .

```

* kmergenie

```bash
BASE_NAME=Bcer
cd ${HOME}/data/anchr/${BASE_NAME}

mkdir -p 2_illumina/kmergenie
cd 2_illumina/kmergenie

kmergenie -l 21 -k 151 -s 10 -t 8 ../R1.fq.gz -o oriR1
kmergenie -l 21 -k 151 -s 10 -t 8 ../R2.fq.gz -o oriR2

```

## Bcer: combinations of different quality values and read lengths

* qual: 25 and 30