Merge branch 'main' of github.com:cambiotraining/bacterial-genomics

cambiotraining · Jul 19, 2024 · 071f9d4 · 071f9d4
2 parents 71ff070 + 2ec8010
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diff --git a/.DS_Store b/.DS_Store
diff --git a/course_files/scripts/.DS_Store b/course_files/scripts/.DS_Store
diff --git a/materials/.DS_Store b/materials/.DS_Store
diff --git a/materials/02-preparing_data.md b/materials/02-preparing_data.md
@@ -29,7 +29,7 @@ We have a lot to fit in this week, and during testing, we found that running all
 
 ### Data
 
-Your analysis starts with FASTQ files (if you need a reminder of what a FASTQ file is, look at the [Intro to NGS > FASTQ](02-intro_ngs.html#FASTQ_Files) section of the materials). The Illumina files come as compressed FASTQ files (`.fastq.gz` format) and there's two files per sample, corresponding to read 1 and read 2. 
+Your analysis starts with FASTQ files (if you need a reminder of what a FASTQ file is, look at the [Intro to NGS > FASTQ](03-intro_ngs.html#FASTQ_Files) section of the materials). The Illumina files come as compressed FASTQ files (`.fastq.gz` format) and there's two files per sample, corresponding to read 1 and read 2. 
 This is indicated by the file name suffix: 
 
 - `*_1.fastq.gz` for read 1

diff --git a/materials/30-poppunk.md b/materials/30-poppunk.md
@@ -49,7 +49,7 @@ To run PopPUNK on our assemblies, the following commands can be used:
 mkdir -p results/poppunk
 
 # run PopPUNK
-poppunk_assign --db GPS_v8_ref --external-clustering GPS_v8_external_clusters.csv --query qfile.txt --output results/poppunk --threads 8
+poppunk_assign --db GPS_v8_ref --external-clustering GPS_v8_external_clusters.csv --query assemblies.txt --output results/poppunk --threads 8
 ```
 The options we used are: