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do
    echo "==> ${d}"
    if [ -e ${d}/work1/superReadSequences.fasta ];
    then
        continue     
    fi

    pushd ~/data/test/rhodobacter_PE_SJ_Sanger4 > /dev/null
    $HOME/share/MaSuRCA/bin/masurca sr_config.txt
    bash assemble.sh
    popd > /dev/null
done
```

### Rhodobacter sphaeroides with `anchr superreads`

```bash
# gzip original fastq
mkdir -p ~/data/test/rhodobacter/PEgz
gzip -c ~/data/test/rhodobacter/PE/frag_1.fastq > ~/data/test/rhodobacter/PEgz/frag_1.fq.gz
gzip -c ~/data/test/rhodobacter/PE/frag_2.fastq > ~/data/test/rhodobacter/PEgz/frag_2.fq.gz

mkdir -p ~/data/test/rhodobacter_superreads
cd ~/data/test/rhodobacter_superreads

perl ~/Scripts/sra/superreads.pl \
    ~/data/test/rhodobacter/PEgz/frag_1.fq.gz \
    ~/data/test/rhodobacter/PEgz/frag_2.fq.gz \
    -s 180 -d 20

```

### 结果比较

```bash
cd ~/data/test/

printf "| %s | %s | %s | %s | %s | %s | %s | %s |\n" \
    "Name" "N50SR" "#SR" "N50Contig" "#Contig" "N50Scaffold" "#Scaffold" "EstG" \
    > stat.md
printf "|:--|--:|--:|--:|--:|--:|--:|--:|\n" >> stat.md

for d in rhodobacter_PE_SJ_Sanger4 rhodobacter_PE_SJ_Sanger rhodobacter_PE_SJ rhodobacter_PE_Sanger4 rhodobacter_PE_Sanger rhodobacter_PE rhodobacter_superreads;
do
    printf "| %s | %s | %s | %s | %s | %s | %s | %s |\n" \
        ${d} \
        $( faops n50 -H -N 50 -C ${d}/work1/superReadSequences.fasta ) \
        $( faops n50 -H -N 50 -C ${d}/CA/10-gapclose/genome.ctg.fasta ) \
        $( faops n50 -H -N 50 -C ${d}/CA/10-gapclose/genome.scf.fasta ) \
        $( cat ${d}/environment.sh \
            | perl -n -e '/ESTIMATED_GENOME_SIZE=\"(\d+)\"/ and print $1' )
done >> stat.md

cat stat.md
```

| name          | N50SR |  #SR | N50Contig | #Contig | N50Scaffold | #Scaffold |    EstG |
|:--------------|------:|-----:|----------:|--------:|------------:|----------:|--------:|
| PE_SJ_Sanger4 |  4586 | 4187 |    205225 |      69 |     3196849 |        35 | 4602968 |
| PE_SJ_Sanger  |  4586 | 4187 |     63274 |     141 |     3070846 |        28 | 4602968 |
| PE_SJ         |  4586 | 4187 |     43125 |     219 |     3058404 |        59 | 4602968 |
| PE_Sanger4    |  4705 | 4042 |    125228 |      67 |      534852 |        30 | 4595684 |
| PE_Sanger     |  4705 | 4042 |     19435 |     412 |       21957 |       359 | 4595684 |
| PE            |  4705 | 4043 |     20826 |     407 |       34421 |       278 | 4595684 |
| superreads    |  4705 | 4043 |           |         |             |           | 4595684 |

有足够多的 long reads 支持下, 不需要 short jump.

# SuperReads 3.1.3

2017 年 2 月, UMD ftp 上多了一个新程序
[SuperReads_RNA](ftp://ftp.genome.umd.edu/pub/MaSuRCA/beta/SuperReads_RNA-1.0.1.tar.gz), 是 MaSuRCA
3.2.1 的简化版. 很可能是 `StringTie` 用了 super-reads 来处理 RNA-seq, 在很多人的要求下做的.

根据这个版本, 我将 MaSuRCA 3.1.3 简化, 去掉所有的依赖, 去掉配合 `Celera Assembler` 的部分, 只留下了
`SuperReads`, 可以用 `Linuxbrew` 安装.

```bash
brew install homebrew/science/jellyfish
brew install wang-q/tap/quorum@1.1.1
brew install wang-q/tap/superreads
```

# Super-reads and anchors

## E. coli: link anchors

```bash
cd ~/zlc/Ecoli/anchorAlign

for id in 0_11 10_13 11_7 12_3 13_33 14_8 15_11 16_20 17_4 18_17 19_19 1_4 20_15 21_13 22_8 23_15 24_34 25_8 26_3 27_30 28_2 29_13 2_27 30_25 31_15 32_28 33_2 34_16 35_3 36_23 37_5 38_29 39_5 3_12 40_9 41_19 4_5 5_7 6_56 7_12 8_15 9_6;
do
    bash ~/Scripts/cpan/App-Anchr/share/link_anchor.sh ${id}.anchor.fasta ${id}.pac.fasta ${id};
    GROUP_COUNT=$(id=${id} perl -e '@p = split q{_}, $ENV{id}; print $p[1];')
    perl ~/Scripts/cpan/App-Anchr/share/ovlp_layout.pl ${id}.ovlp.tsv --range "1-${GROUP_COUNT}"
done

# Exceeded memory bound: 502169772
#poa -preserve_seqorder -read_fasta 9_2.renamed.fasta -clustal 9_2.aln -hb ~/Scripts/sra/poa-blosum80.mat 

#cp 9_2.renamed.fasta myDB.pp.fasta
#
#DBrm myDB
#fasta2DB myDB myDB.pp.fasta
#DBdust myDB
#
#if [ -e myDB.las ]; then
#    rm myDB.las
#fi
#HPC.daligner myDB -v -M4 -e.70 -l1000 -s1000 -mdust > job.sh
#bash job.sh
#rm job.sh
#
#LA4Falcon -o myDB.db myDB.las 1-2
#
#perl ~/Scripts/sra/las2ovlp.pl 9_2.renamed.fasta <(LAshow -o myDB.db myDB.las 1)
#
#perl ~/Scripts/sra/las2ovlp.pl 9_2.renamed.fasta 9_2.show.txt -r 9_2.replace.tsv


# 3 5 10 8 4 9 7 2 11 6 1
perl ~/Scripts/egaz/sparsemem_exact.pl \
    -f 0_11.renamed.fasta -g ~/data/dna-seq/e_coli/superreads/NC_000913.fa \
    --length 500 -o 0_11.chr.tsv
perl ~/Scripts/sra/ovlp_layout.pl 0_11.ovlp.tsv --range 1-11