# Genome assembly for Arion vulgaris

Challenge:
**big genome size**: ~1.5G
**limited sequencing coverage and long reads**:
WGS:~53G
10X genomics:128G
Nanopore:16.5G
**high heterozygosity**:1%

## assemble use only Nanopore reads
### [Canu](https://canu.readthedocs.io/en/latest/quick-start.html)
#### Correct: correct nanopore/pacbio reads

canu -correct \ 
    -p arion \ #output prefix
    -d nano_arion \ #output dir name 
    genomeSize=1500m \ #genome size
    corMinCoverage=0 \ #corMinCoverage=0 will keep all reads, defult is 4
    correctedErrorRate=0.16 \ #set to 0.16 when sequencing coverage is less then 30X
    -nanopore-raw nanopore.fasta.gz

##### Trim: trim reads

canu -trim \
        -p arion -d nano_arion
        genomeSize=1500m
        -nanopore-corrected
        nano_arion/arion.correctedReads.fasta.gz

#### Assemble for high heterozygosity genome

# error rate 0.035
canu -assemble \
    -p arion -d arion-erate-0.035 \
    genomeSize=1500m\
    correctedErrorRate=0.035 \
    -nanoporecorrected nano_arion/arion.trimmedReads.fasta.gz

#### Another way use batOption to phase and assembly(for high heterozygosity)

canu \
 -p arion -d nano_arion \
 genomeSize=1500m \
 corOutCoverage=200 "batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50" \
-nanopore-raw nanopore.fasta.gz

#### Reference
https://www.jianshu.com/p/66d859f7643f
### [NextDenovo](https://github.com/Nextomics/NextDenovo/blob/master/doc/OPTION.md)
#### NextCorrect

#### NextGraph

#### Reference
https://www.jianshu.com/p/fa26792435eb
https://wap.sciencenet.cn/blog-3406804-1204832.html?mobile=1

### [MECAT](https://github.com/xiaochuanle/MECAT)

#### Reference
https://www.grandomics.com/science_articles/s_d_s_j_f_x_x_g_j_mecat_j_c_k_b_d_x_z/