ENH update read the docs

Author: psj1997

docs/subcommands.md

@@ -19,6 +19,7 @@ Reconstruct bins with single or co-assembly binning using one command.
 * `-i/--input-fasta` : Path to the input contig fasta file (`gzip` and `bzip2` compression are accepted).
 * `-b/--input-bam`: Path to the input BAM (`.bam` extension)  or CRAM (`.cram`) files. You can pass multiple BAM files, one per sample.
 * `-o/--output`: Output directory (will be created if non-existent).
+* `-a/--abundance` Path to the abundance file from strobealign-aemb. This can only be used when samples used in binning above or equal 5.
 
 #### Recommended arguments
 
@@ -126,6 +127,7 @@ These are the are same as for `single_easy_bin`.
 * `--ml-threshold`
 * `--taxonomy-annotation-table`
 * `--tmpdir`
+* `-a/--abundance`
 
 These are the are same as for `single_easy_bin`.
 
@@ -138,6 +140,7 @@ The subcommand `generate_sequence_features_single` requires the contig file and
 * `-i/--input-fasta`
 * `-b/--input-bam`
 * `-o/--output`
+* `-a/--abundance`
 
 These are the are same as for `single_easy_bin`.
 
@@ -161,6 +164,7 @@ The subcommand `generate_sequence_features_multi` requires the combined contig f
 * `-i/--input-fasta`
 * `-o/--output`
 * `-b/--input-bam`
+* `-a/--abundance`
 
 These are the same as for `multi_easy_bin`.
 

docs/usage.md

@@ -419,3 +419,29 @@ SemiBin2 generate_cannot_links -i S5.fa -o S5_output
 
 See the comment above about how you can bypass most of the computation if you have run `mmseqs2` to annotate your contigs against GTDB already.
 
+
+## Running SemiBin with strobealign-aemb
+
+Strobealign-aemb is a fast abundance estimation method for metagenomic binning. 
+As strobealign-aemb can not provide the mapping information for every position of the contig, so we can not run SemiBin2 with strobealign-aemb in binning modes where samples used smaller 5 and need to split the contigs to generate the must-link constratints. 
+
+
+1. Split the fasta files 
+```bash
+python script/generate_split.py -c contig.fa -o output
+```
+2. Map reads using [strobealign-aemb](https://github.com/ksahlin/strobealign) to generate the abundance information
+```bash
+strobealign --aemb output/split.fa read1_1.fq read1_2.fq -R 6 > sample1.txt
+strobealign --aemb output/split.fa read2_1.fq read2_2.fq -R 6 > sample2.txt
+strobealign --aemb output/split.fa read3_1.fq read3_2.fq -R 6 > sample3.txt
+strobealign --aemb output/split.fa read4_1.fq read4_2.fq -R 6 > sample4.txt
+strobealign --aemb output/split.fa read5_1.fq read5_2.fq -R 6 > sample5.txt
+```
+3. Run SemiBin2 (like running SemiBin with BAM files)
+```bash
+SemiBin2 generate_sequence_features_single -i contig.fa -a *.txt -o output
+SemiBin2 generate_sequence_features_multi -i contig.fa -a *.txt -s : -o output
+SemiBin2 single_easy_bin -i contig.fa -a *.txt -o output
+SemiBin2 multi_easy_bin i contig.fa -a *.txt -s : -o output
+