updates project3

docs/course_material/group_work/project3.md

@@ -10,20 +10,32 @@ There are eight different species: `sample_[1-8].fastq.gz`
 
 
 
-Each species has a fastq file available. Download only the data for the species that you will require: 
+Each species has a fastq file available. You can download all fastq files like this: 
 
 ```sh
-mkdir -p ~/workdir/groupwork_assembly
-cd ~/workdir/groupwork_assembly
+wget https://ngs-longreads-training.s3.eu-central-1.amazonaws.com/project3.tar.gz
+tar -xvf project3.tar.gz
+rm project3.tar.gz
+```
+
+!!! note
+    Download the data file package in your shared working directory, i.e. : `/group_work/<group name>` or `~/<group name>`. Only one group member has to do this.
 
-# change this to your species:
-species="sample_1"
+This will create a directory `project3` with the following structure:
 
-wget https://ngs-longreads-training.s3.eu-central-1.amazonaws.com/group_work_assembly/"$species".fastq.gz
-tar -xvf "$species".fastq.gz
-rm "$species".fastq.gz
 ```
-
+project3
+|-- sample_1.fastq.gz
+|-- sample_2.fastq.gz
+|-- sample_3.fastq.gz
+|-- sample_4.fastq.gz
+|-- sample_5.fastq.gz
+|-- sample_6.fastq.gz
+|-- sample_7.fastq.gz
+`-- sample_8.fastq.gz
+
+0 directories, 8 files
+```
 
 ### Before you start
 
@@ -46,13 +58,34 @@ You can start this project with dividing the species over the different group me
     conda activate assembly
     ```
 
-
 * Perform a quality control with `NanoPlot`.
     * How is the read quality? Is this quality expected?
     * How is the read length?
 * Perform an assembly with `flye`. 
     * Have a look at the helper first with `flye --help`. Make sure you pick the correct mode (i.e. `--pacbio-??`). 
     * Check out the output. Where is the assembly? How is the quality? For that, check out `assembly_info.txt`. 
+    * What species did you assemble? Choose from this list:
+    ```
+    Acinetobacter baumannii
+    Bacillus cereus
+    Bacillus subtilis
+    Burkholderia cepacia
+    Burkholderia multivorans
+    Enterococcus faecalis
+    Escherichia coli
+    Helicobacter pylori
+    Klebsiella pneumoniae
+    Listeria monocytogenes
+    Methanocorpusculum labreanum
+    Neisseria meningitidis
+    Rhodopseudomonas palustris
+    Salmonella enterica
+    Staphylococcus aureus
+    Streptococcus pyogenes
+    Thermanaerovibrio acidaminovorans
+    Treponema denticola
+    Vibrio parahaemolyticus
+    ```
     * Did flye assemble any plasmid sequences?
 * Check the completeness with `BUSCO`. Have a good look at the manual first. You can use automated lineage selecton by specifying `--auto-lineage-prok`. After you have run `BUSCO`, you can generate a nice completeness plot with `generate_plot.py`. You can check its usage with `generate_plot.py --help`. 
     * How is the completeness? Is this expected?

scripts/generate_data_project3/download_reads.sh

@@ -0,0 +1,7 @@
+for BC in bc2001 bc2002 bc2004 bc2007 bc2011 bc2019 bc2022 bc2015
+do
+    wget -O "$BC".bam https://downloads.pacbcloud.com/public/dataset/2021-11-Microbial-96plex/demultiplexed-reads/m64004_210929_143746."${BC}".bam
+    samtools fastq -0 "$BC".fastq "$BC".bam
+    gzip "$BC".fastq
+done
+

scripts/generate_data_project3/lookup_bc_organism.csv

@@ -0,0 +1,8 @@
+bc2001,sample_6
+bc2002,sample_7
+bc2004,sample_3
+bc2007,sample_1
+bc2011,sample_5
+bc2019,sample_2
+bc2022,sample_8
+bc2015,sample_4

scripts/generate_data_project3/rename_fastq.sh

@@ -0,0 +1,4 @@
+sed 's/,/ /g' lookup_bc_organism.csv | while read BC NAME
+do
+    mv "$BC".fastq.gz "$NAME.fastq.gz"
+done

scripts/project2_commands.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-cd ~/workdir/groupwork_pacbio/
+cd ~/workdir/project2/
 
 # generate reference for minimap2
 minimap2 \