Commit c99c2033 authored by peguerin's avatar peguerin
Browse files

readme update

parent 9dbabac9
......@@ -73,20 +73,25 @@ with `pe-dir` as a folder of paired-end sequencing results, `me-dir` as mate-pai
# Genome assembly methods
## Platanus
Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.
### 1. Contig assembling
```
platanus assemble -tmp temp/ -m 256 -t 64 -o serran_assemble -f pe-dir/*.fastq 2> assemble.log
```
### assemble contig
fff
### 2. Scaffoling
### 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
```
fff
### gapclose
### 3. Gapclose
fff
## Superstar
## Supernova
......@@ -107,14 +112,16 @@ _Mullus surmuletus_ | Platanus | MBB | Paired-end 35
_Mullus surmuletus_ | Platanus | MESO@LR | Paired-end 350bp & 550bp insert size Mate-pair 3Kbp & 5Kbp insert size | 3146055 | 384 | 613 | 2940 | 488370 | 74X
_Mullus surmuletus_ | Abyss2 | MBB | Paired-end 350bp & 550bp insert size Mate-pair 3Kbp & 5Kbp insert size | 36011115 | 96 | 686 | 4938 | 17739 | 66X
_Serranus cabrilla_ | Platanus | MBB | Paired-end 350bp & 550bp insert size Mate-pair 3Kbp & 5Kbp insert size | 2169385 | 1135 | 627 | 2190 | 613541 | 63X
_Serranus cabrilla_ | Supernova | MESO@LR | Chromium Linked-reads | NA | NA | 223 * | 4951 * | 67074 * | :question:
_Serranus cabrilla_ | `Supernova` | Both | `Chromium Linked-reads` | NA | NA | `223` | `4951` | `67074` | 48X
_Serranus cabrilla_ | ARCS | MBB | Both | NA | NA | 627 | 2122 | 624679 | 63X
- Species : the species of the organism we sequenced
- 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 and [MESO@LR](https://meso-lr.umontpellier.fr/) is 80 cores and 1To Ram
- Library : see [data description](#-data-files)
- 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
- 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
- Number of scaffolds : number of set of linked-contigs
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment