Commit 99be2411 authored by peguerin's avatar peguerin
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rename supernova

parent f39947d1
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A collection of commands to assemble genome from NGS data.
## Prerequisites
* [platanus 1.2.4](http://platanus.bio.titech.ac.jp/)
* [supernova 2.1.1](https://support.10xgenomics.com/de-novo-assembly/software/downloads/latest)
* [longranger 2.2.2](https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger)
* [arcs](https://github.com/bcgsc/arcs) please follow instruction into [install.sh](arcs/install.sh)
# Data files
NGS data are stored
## Description
We aims to assemble 3 _de novo_ draft genomes of one invididual of 3 different species
- _Diplodus sargus_ that we refers as `sar`
- _Mullus surmuletus as `mullus`
- _Serranus cabrilla_ as `serran`
The three draft genomes were sequenced within the NGS technology.
### paired-end
* For each genome, two paired-end libraries with insert sizes of 350 bp and 550 bp.
* They are sequenced as 150 paired-end base reads on a Illumina HiSeq 4000 sequencer.
* There was 1-2 µg in a total volume of 50 µL for each of the samples in the paired-end libraries.
* Library preparation and sequencing was performed by [FASTERIS](https://www.fasteris.com/dna/)
### mate-pair
* For each genome, two mate-pair libraries with insert sizes of 3 kbp and 5 kbp were constructed.
* They are sequenced as 150 paired-end base reads on a Illumina HiSeq 4000 sequencer.
* There was 4 µg of DNA in a total volume of 50 µL for the samples used to build the mate-pair libraries.
* Library preparation and sequencing was done by [FASTERIS](https://www.fasteris.com/dna/)
### 10X Genomics
* For _Serranus cabrilla_, a linked-reads library from the Chromium technology were performed.
* They require high molecular weight DNA: samples had to contain no less than 10 µg DNA, with a concentration of 110 ng/µl. Approximately 1 ng of HMW DNA was processed on a 10X Chromium instrument to prepare barcoded libraries.
* These libraries were sequenced on an Illumina HiSeq 2500 machine.
* Library preparation and sequencing was performed by [MGX](https://www.mgx.cnrs.fr).
## Set the initial directory structure
main folder
- pedir
- pe-dir
- 180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
- 180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
- 180802_NB501473_A_L1-4_ANIZ-2_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
- 180802_NB501473_A_L1-4_ANIZ-2_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq
- medir
- me-dir
- 180806_NB501850_A_L1-4_ANIZ-3_R1.fastq
- 180806_NB501850_A_L1-4_ANIZ-3_R2.fastq
- 180807_NB501850_A_L1-4_ANIZ-4_R1.fastq
- 180807_NB501850_A_L1-4_ANIZ-4_R2.fastq
- xdir
- x-dir
- Lib_10_S1_L002_I1_001.fastq
- Lib_10_S1_L002_R1_001.fastq
- Lib_10_S1_L002_R2_001.fastq
## Prerequisites
* [platanus 1.2.4](http://platanus.bio.titech.ac.jp/)
* [supernova 2.1.1](https://support.10xgenomics.com/de-novo-assembly/software/downloads/latest)
* [longranger 2.2.2](https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger)
* [arcs](https://github.com/bcgsc/arcs) please follow instruction into [install.sh](arcs/install.sh)
# Genome assembly methods
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## Arcs
## Measuring the assembly
# Results
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