Commit 2596f2db authored by peguerin's avatar peguerin
Browse files

readme update

parent c99c2033
......@@ -85,7 +85,7 @@ platanus assemble -tmp temp/ -m 256 -t 64 -o serran_assemble -f pe-dir/*.fastq 2
### 2. Scaffoling
```
platanus scaffold -t 80 -tmp temp/ -c serran_assemble_contig.fa -b serran_assemble_contigBubble.fa -IP1 me-dir/*ANIZ-3*.fastq -IP2 me-dir/*ANIZ-3*.fastq -OP3 -OP4 /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq 2> scaffold.log
platanus scaffold -t 80 -tmp temp/ -c serran_assemble_contig.fa -b serran_assemble_contigBubble.fa -IP1 me-dir/*ANIZ-3*.fastq -IP2 me-dir/*ANIZ-3*.fastq -OP3 -OP4 pe-dir/*ANIZ-2*.fastq /media/bigvol/peguerin/rawdata/fasteris/ANIZ-1-2/data/180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq 2> scaffold.log
```
### 3. Gapclose
......@@ -120,7 +120,7 @@ _Serranus cabrilla_ | ARCS | MBB | Both
- Genome assembler : the software/workflow we used to perform genome assembly
- Computing platform : The high performance platform we used to perform genome assembly
* [MBB](https://mbb.univ-montp2.fr/MBB/index.php) is 64 cores and 512Go RAM
* [MESO@LR](https://meso-lr.umontpellier.fr/) is 80 cores and 1To Ram
* [MESO@LR](https://meso-lr.umontpellier.fr/) is 80 cores and 1To RAM
- Library : see [data description](#data-files)
- Number of contigs : number of set of overlapping DNA segments
- Contig N50 : size of the contigs from which contigs which are larger represents half of the total genome size
......
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