profile: update doc

shenwei356 · Mar 7, 2022 · 9846929 · 9846929
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diff --git a/benchmarks/real-pathogen-gu2020/README.md b/benchmarks/real-pathogen-gu2020/README.md
@@ -46,7 +46,7 @@ We download the 99 Illumina short-reads datasets from [PRJNA558701](https://www.
 in which 92 samples has detailed information in the supplementary table 1.
 And 87 samples are verified by culture or 16S rRNA gene qPCR.
 
-Run accession and corresponding sample names are listed in [acc2sample.tsv](https://github.com/shenwei356/kmcp/blob/main/benchmarks/pathogen-gu2020/acc2sample.tsv).
+Run accession and corresponding sample names are listed in [acc2sample.tsv](https://github.com/shenwei356/kmcp/blob/main/benchmarks/real-pathogen-gu2020/acc2sample.tsv).
 
 Download reads using SRAtoolkit:
 

diff --git a/docs/tutorial/profiling/index.md b/docs/tutorial/profiling/index.md
@@ -447,7 +447,9 @@ Using this flag will override the relevant options.
 
 **Supported profiling output formats**:
 
-- KMCP      (`-o/--out-prefix`)
+- KMCP      (`-o/--out-prefix`). 
+  **Note that: abundances are only computed for target references rather than
+     each taxon at all taxonomic ranks, so please output CAMI or MetaPhlAn format**.
 - CAMI      (`-M/--metaphlan-report`, `--metaphlan-report-version`, sample name: `-s/--sample-id`, taxonomy data: `--taxonomy-id`)
 - MetaPhlAn (`-C/--cami-report`, sample name: `-s/--sample-id`))
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -486,13 +486,21 @@ Performance notes:
      lines proceeded by a thread can be set by the flag --line-chunk-size.
   2. However using a lot of threads does not always accelerate
      processing, 4 threads with a chunk size of 500-5000 is fast enough.
-  3. If the stage 1/4 produces thousands of candidates, then the stage 2/4
+ *3. If the stage 1/4 produces thousands of candidates, then the stage 2/4
      would be very slow. You can use the flag --no-amb-corr to disable
      ambiguous reads correction which has very little effect on the results.
 
 Profiling output formats:
   1. KMCP      (-o/--out-prefix)
-  2. CAMI      (-M/--metaphlan-report, --metaphlan-report-version, -s/--sample-id, --taxonomy-id)
+     Note that: abundances are only computed for target references rather than
+     each taxon at all taxonomic ranks, so please output CAMI or MetaPhlAn format.
+  2. CAMI      (-M/--metaphlan-report, --metaphlan-report-version,
+                -s/--sample-id, --taxonomy-id)
+     Related tools (https://github.com/shenwei356/taxonkit):
+       - taxonkit profile2cami: convert any metagenomic profile table with
+         TaxIds to CAMI format. Use this if you forget to output CAMI format.
+       - taxonkit cami-filter: remove taxa of given TaxIds and their
+         descendants in CAMI metagenomic profile.
   3. MetaPhlAn (-C/--cami-report, -s/--sample-id)
 
 KMCP format:

diff --git a/kmcp/cmd/profile.go b/kmcp/cmd/profile.go
@@ -123,13 +123,21 @@ Performance notes:
      lines proceeded by a thread can be set by the flag --line-chunk-size.
   2. However using a lot of threads does not always accelerate
      processing, 4 threads with a chunk size of 500-5000 is fast enough.
-  3. If the stage 1/4 produces thousands of candidates, then the stage 2/4
+ *3. If the stage 1/4 produces thousands of candidates, then the stage 2/4
      would be very slow. You can use the flag --no-amb-corr to disable
      ambiguous reads correction which has very little effect on the results.
 
 Profiling output formats:
   1. KMCP      (-o/--out-prefix)
-  2. CAMI      (-M/--metaphlan-report, --metaphlan-report-version, -s/--sample-id, --taxonomy-id)
+     Note that: abundances are only computed for target references rather than
+     each taxon at all taxonomic ranks, so please output CAMI or MetaPhlAn format.
+  2. CAMI      (-M/--metaphlan-report, --metaphlan-report-version,
+                -s/--sample-id, --taxonomy-id)
+     Related tools (https://github.com/shenwei356/taxonkit):
+       - taxonkit profile2cami: convert any metagenomic profile table with
+         TaxIds to CAMI format. Use this if you forget to output CAMI format.
+       - taxonkit cami-filter: remove taxa of given TaxIds and their
+         descendants in CAMI metagenomic profile.
   3. MetaPhlAn (-C/--cami-report, -s/--sample-id)
 
 KMCP format: