update doc

shenwei356 · Jun 13, 2023 · 5a0dc93 · 5a0dc93
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diff --git a/docs/tutorial/detecting-pathogens/index.md b/docs/tutorial/detecting-pathogens/index.md
@@ -80,7 +80,7 @@ Creating the taxid mapping file (only needed for multiple reference genomes).
 
 ## Searching reads against the KMCP database
 
- kmcp search -d refs.kmcp/ sample_1.fq.gz sample_2.fq.gz -o sample.kmcp.tsv.gz
+ kmcp search -w -d refs.kmcp/ sample_1.fq.gz sample_2.fq.gz -o sample.kmcp.tsv.gz
 
 ## Profiling
 

diff --git a/docs/tutorial/index.md b/docs/tutorial/index.md
@@ -1,4 +1,5 @@
 # Tutorials
 
 - [Taxonomic profiling](profiling)
-- [Sequence and genome searching](searching)
+- [Detecting specific pathogens](detecting-pathogens)
+- [Sequence and genome searching](searching)
diff --git a/docs/tutorial/profiling/index.md b/docs/tutorial/profiling/index.md
@@ -22,6 +22,7 @@ For example, removing adapters and trimming using [fastp](https://github.com/Ope
  fastp -i in_1.fq.gz -I in_2.fq.gz \
   -o out_1.fq.gz -O out_2.fq.gz \
   -l 75 -q 20 -W 4 -M 20 -3 20 --thread 32 \
+  --trim_poly_g --poly_g_min_len 10 --low_complexity_filter \
   --html out.fastp.html
 
 ### Step 2. Removing host reads
@@ -30,24 +31,21 @@ Tools:
 
 - [bowtie2](https://github.com/BenLangmead/bowtie2) is [recommended](https://doi.org/10.1099/mgen.0.000393) for removing host reads.
 - [samtools](https://github.com/samtools/samtools) is also used for processing reads mapping file.
-- [pigz](https://zlib.net/pigz/) is a parallel implementation of `gzip`, which is much faster than `gzip`.
 
 Host reference genomes:
 
 - Human: [CHM13](https://github.com/marbl/CHM13). We also provide a database of CHM13 for fast removing human reads.
 
 Building the index (~60min):
 
- bowtie2-build --threads 32 GCA_009914755.3_CHM13_T2T_v1.1_genomic.fna.gz chm13
+ bowtie2-build --threads 32 GCA_009914755.4_T2T-CHM13v2.0_genomic.fna.gz chm13v2.0
 
 Mapping and removing mapped reads:
 
- index=~/ws/db/bowtie2/chm13
+ index=~/ws/db/bowtie2/chm13v2.0
 
- bowtie2 --threads 32 -x $index -1 in_1.fq.gz -2 in_2.fq.gz \
-  | samtools view -buS -f 4 - \
-  | samtools fastq - \
-  | gzip -c > sample.fq.gz
+ bowtie2 --threads 32 -x $index -1 in_1.fq.gz -2 in_2.fq.gz \
+  | samtools fastq -f 4 -o sample.fq.gz -
 
 ### Step 3. Searching
 
@@ -209,7 +207,7 @@ Demo result:
 
 #### Searching on a computer cluster
 
-Update: We recommend analyzing one sample using one computer node, which is easier to setup up.
+<p style="color:Tomato;">Update: We recommend analyzing one sample using one computer node, which is easier to setup up.</p>
 
 
 Here, we split genomes of GTDB into 16 partitions and build a database for 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -7,8 +7,8 @@ nav:
 - Usage: usage.md
 - Tutorials:
  - Taxonomic profiling: tutorial/profiling/index.md
- - Sequence and genome searching: tutorial/searching/index.md
  - Detecting specific pathogens: tutorial/detecting-pathogens/index.md
+ - Sequence and genome searching: tutorial/searching/index.md
 - Benchmarks:
  - Taxonomic profiling: benchmark/profiling/index.md
  - Sequence and genome searching: benchmark/searching/index.md