update docs

README.md

@@ -35,7 +35,3 @@ By the end of this session you will be able to:
 
     If you don't meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.
 
-## Training material
-
-Gfastats examples can be found [here](https://github.com/BGAcademy23/gfastar/docs/gfastats.md).
-Kreeq examples can be found [here](https://github.com/BGAcademy23/gfastar/docs/kreeq.md).

docs/README.md

@@ -10,6 +10,9 @@ Research Assistant Professor, The Rockefeller University
 Cassidy Johnson  
 Graduate Fellow, The Rockefeller University
 
+Jack Medico
+Graduate Fellow, The Rockefeller University
+
 ## Description
 
 By the end of this session you will be able to:
@@ -19,10 +22,6 @@ By the end of this session you will be able to:
 3. Compute QV estimates using kreeq
 4. Evaluate genome assemblies at scale using Buttercup
 
-## Slides
-
-[Click here to see slides](https://slides.google.com)
-
 ## Prerequisites
 
 1. Understanding basic terms in genome assembly, such as reads, contigs, scaffolds, ...
@@ -35,3 +34,9 @@ By the end of this session you will be able to:
     Please also read the description carefully to see if this session is relevant to you.
 
     If you don't meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.
+
+## Training material
+
+Gfastats examples can be found [here](gfastats.md).
+
+Kreeq examples can be found [here](kreeq.md).

docs/gfastats.md

@@ -1,85 +1,169 @@
 Help:
-`gfastats -h`
+```
+gfastats -h
+```
 File:
-cat testFiles/random1.fasta `
+```
+cat testFiles/random1.fasta
+```
 Summary statistics:
-`gfastats testFiles/random1.fasta`
+```
+gfastats testFiles/random1.fasta
+```
 Tabular output:
-`gfastats testFiles/random1.fasta -t`
+```
+gfastats testFiles/random1.fasta -t
+```
 Change locale:
-`gfastats large_input.fasta.gz --locale en_US.UTF-8`
+```
+gfastats large_input.fasta.gz --locale en_US.UTF-8
+```
 Full output:
-`gfastats testFiles/random1.fasta --nstar-report`
+```
+gfastats testFiles/random1.fasta --nstar-report
+```
 Report by sequence:
-`gfastats testFiles/random1.fasta --seq-report`
+```
+gfastats testFiles/random1.fasta --seq-report
+```
 Original file:
-`gfastats testFiles/random1.fasta -ofa`
+```
+gfastats testFiles/random1.fasta -ofa
+```
 Line length:
-`gfastats testFiles/random1.fasta -ofa --line-length 2`
+```
+gfastats testFiles/random1.fasta -ofa --line-length 2
+```
 Subset:
-`gfastats testFiles/random1.fasta Header2 -ofa`
+```
+gfastats testFiles/random1.fasta Header2 -ofa
+```
 Subset with bed:
-`gfastats testFiles/random1.fasta -e <(echo Header2) -ofa`
+```
+gfastats testFiles/random1.fasta -e <(echo Header2) -ofa
+```
 cat testFiles/random1.fasta.bed`
-`gfastats testFiles/random1.fasta -ofa -e testFiles/random1.fasta.bed`
-`gfastats testFiles/random1.fasta -ofa -i testFiles/random1.fasta.bed`
+```
+gfastats testFiles/random1.fasta -ofa -e testFiles/random1.fasta.bed
+```
+```
+gfastats testFiles/random1.fasta -ofa -i testFiles/random1.fasta.bed
+```
 Size of components:
-`gfastats testFiles/random1.fasta -s s`
-`gfastats testFiles/random1.fasta -s c`
-`gfastats testFiles/random1.fasta -s g`
+```
+gfastats testFiles/random1.fasta -s s
+```
+```
+gfastats testFiles/random1.fasta -s c
+```
+```
+gfastats testFiles/random1.fasta -s g
+```
 AGP:
-`gfastats testFiles/random1.fasta -b a`
+```
+gfastats testFiles/random1.fasta -b a
+```
 BED coordinates:
-`gfastats testFiles/random1.fasta -b s`
-`gfastats testFiles/random1.fasta -b c`
-`gfastats testFiles/random1.fasta -b g`
+```
+gfastats testFiles/random1.fasta -b s
+```
+```
+gfastats testFiles/random1.fasta -b c
+```
+```
+gfastats testFiles/random1.fasta -b g
+```
 Sorting:
-`gfastats testFiles/random1.fasta -ofa --sort largest`
-`gfastats testFiles/random1.fasta -ofa --sort descending`
-`gfastats testFiles/random1.fasta -ofa --sort test.sort`
+```
+gfastats testFiles/random1.fasta -ofa --sort largest
+```
+```
+gfastats testFiles/random1.fasta -ofa --sort descending
+```
+```
+gfastats testFiles/random1.fasta -ofa --sort test.sort
+```
 GFA2:
-`gfastats testFiles/random1.gfa2 -o gfa2`
+```
+gfastats testFiles/random1.gfa2 -o gfa2
+```
 GFA2 to FASTA conversion:
-`gfastats testFiles/random1.gfa2 -o fasta`
+```
+gfastats testFiles/random1.gfa2 -o fasta
+```
 GFA2 to GFA1 conversion:
-`gfastats testFiles/random1.gfa2 -o gfa`
+```
+gfastats testFiles/random1.gfa2 -o gfa
+```
 GFA1:
-`gfastats testFiles/random2.gfa -o gfa`
+```
+gfastats testFiles/random2.gfa -o gfa
+```
 GFA1 to FASTA:
-`gfastats testFiles/random2.gfa -o fasta`
+```
+gfastats testFiles/random2.gfa -o fasta
+```
 GFA1 to GFA2:
-`gfastats testFiles/random2.gfa -o gfa2`
+```
+gfastats testFiles/random2.gfa -o gfa2
+```
 GFA1 no sequence:
-`gfastats testFiles/random2.noseq.gfa -o gfa`
+```
+gfastats testFiles/random2.noseq.gfa -o gfa
+```
 GFA1 no sequence:
-`gfastats testFiles/random2.noseq.gfa -o fa`
+```
+gfastats testFiles/random2.noseq.gfa -o fa
+```
 Homopolymer compression:
-`gfastats testFiles/random1.fasta --homopolymer-compress 1 -ofa`
+```
+gfastats testFiles/random1.fasta --homopolymer-compress 1 -ofa
+```
 Find terminal overlaps:
-`gfastats testFiles/random5.findovl.gfa -ogfa`
-`gfastats testFiles/random5.findovl.gfa --discover-terminal-overlaps 3 -ogfa`
+```
+gfastats testFiles/random5.findovl.gfa -ogfa
+```
+```
+gfastats testFiles/random5.findovl.gfa --discover-terminal-overlaps 3 -ogfa
+```
 Discover paths:
-`gfastats testFiles/random1.fasta -ogfa | grep -v "^P" > test.gfa`
-`gfastats test.gfa -ogfa`
-`gfastats test.gfa -ogfa2 --discover-paths`
+```
+gfastats testFiles/random1.fasta -ogfa | grep -v "^P" > test.gfa
+```
+```
+gfastats test.gfa -ogfa
+```
+```
+gfastats test.gfa -ogfa2 --discover-paths
+```
 Superimpose AGP:
-`gfastats testFiles/random1.fasta -a testFiles/random1.agp -ofa`
+```
+gfastats testFiles/random1.fasta -a testFiles/random1.agp -ofa
+```
 SAK reverse complement:
-`cat testFiles/random1.rvcp.sak`
-`gfastats testFiles/random1.fasta -ofa`
-`gfastats testFiles/random1.fasta -k testFiles/random1.rvcp.sak -ofa`
+```
+cat testFiles/random1.rvcp.sak
+```
+```
+gfastats testFiles/random1.fasta -ofa
+```
+```
+gfastats testFiles/random1.fasta -k testFiles/random1.rvcp.sak -ofa
+```
 Other SAK instructions:
-`cat testFiles/random1.instructions.sak`
-`gfastats testFiles/random1.fasta -ofa`
-`gfastats testFiles/random1.fasta -ofa -k <(head -1 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ofa -k <(head -2 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ofa -k <(head -3 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ofa -k <(head -4 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ogfa2 -k <(head -4 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ofa -k <(head -5 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ogfa2 -k <(head -5 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ofa -k <(head -6 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ogfa2 -k <(head -6 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ogfa2 -k <(head -6 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ogfa2 -k <(head -7 testFiles/random1.instructions.sak)`
-`gfastats testFiles/random1.fasta -ofa -k <(head -8 testFiles/random1.instructions.sak)`
+```
+cat testFiles/random1.instructions.sak
+gfastats testFiles/random1.fasta -ofa
+gfastats testFiles/random1.fasta -ofa -k <(head -1 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ofa -k <(head -2 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ofa -k <(head -3 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ofa -k <(head -4 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ogfa2 -k <(head -4 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ofa -k <(head -5 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ogfa2 -k <(head -5 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ofa -k <(head -6 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ogfa2 -k <(head -6 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ogfa2 -k <(head -6 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ogfa2 -k <(head -7 testFiles/random1.instructions.sak)
+gfastats testFiles/random1.fasta -ofa -k <(head -8 testFiles/random1.instructions.sak)
+```

mkdocs.yml

@@ -3,8 +3,9 @@ edit_uri: https://github.com/bgacademy23/gfastar/blob/main/docs
 
 nav:
     - Home: README.md
+    - gfastats: gfastats.md
+    - kreeq: kreeq.md
     - BGA23: https://bga23.org
-
 theme:
     name: material
     language: en