Commit 810c97ff authored by peguerin's avatar peguerin
Browse files

arcs install

parent 4e5f6a9a
# Genome assemblies collection
A collection of commands to assemble genome from NGS data.
main folder
pedir
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
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
Lib_10_S1_L002_I1_001.fastq
Lib_10_S1_L002_R1_001.fastq
Lib_10_S1_L002_R2_001.fastq
xxx
- pedir
- 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
- 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
- Lib_10_S1_L002_I1_001.fastq
- Lib_10_S1_L002_R1_001.fastq
- Lib_10_S1_L002_R2_001.fastq
......@@ -39,8 +39,12 @@ pip3 install intervaltree pybedtools pysam statistics
git clone https://github.com/bcgsc/tigmint
echo "export PATH=$PATH:/media/bigvol/peguerin/tigmint/bin" >> ~/.bashrc
## install pigz
sudo apt install pigz
brew tap brewsci/bio
wget http://www.bcgsc.ca/downloads/supplementary/ARCS/testdata/links_c5r0.05e30000-l5-a0.9.scaffolds.fa
\ No newline at end of file
wget http://www.bcgsc.ca/downloads/supplementary/ARCS/testdata/links_c5r0.05e30000-l5-a0.9.scaffolds.fa
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