working on section "Full-Genome Alignment"

found an apparent bug in paftools.js call. To debug...

cookbook.md

@@ -5,6 +5,9 @@
   * [Mapping long reads](#map-pb)
   * [Mapping Illumina paired-end reads](#map-sr)
   * [Evaluating mapping accuracy with simulated reads (for developers)](#mapeval)
+- [Full-Genome Alignment](#genome-aln)
+  * [Intra-species assembly alignment](#asm-to-ref)
+  * [Calling variants from assembly-to-reference alignment](#asm-var)
 - [Read Overlap](#read-overlap)
   * [Long-read overlap](#long-read-overlap)
   * [Evaluating overlap sensitivity (for developers)](#ov-eval)
@@ -39,7 +42,7 @@ line. **Please always make sure you are using an intended pre-built index.**
 
 ### <a name="map-sr"></a>Mapping Illumina paired-end reads:
 ```sh
-minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq > mapped-sr.sam
+minimap2 -ax sr -t4 ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq > mapped-sr.sam
 ```
 
 ### <a name="mapeval"></a>Evaluating mapping accuracy with simulated reads (for developers)
@@ -78,6 +81,50 @@ paftools.js mason2fq tmp.sam | seqtk seq -1 > ecoli_mason_2.fq
 
 
 
+## <a name="genome-aln"></a>Full-Genome Alignment
+
+### <a name="asm-to-ref"></a>Intra-species assembly alignment
+```sh
+minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa > ecoli_canu.paf
+```
+Here `ecoli_canu.fa` is the Canu assembly of `ecoli_p6_25x_canu.fa`. This
+command line outputs alignments in the [PAF format][paf]. Use `-a` instead of
+`-c` to get output in the SAM format.
+
+### <a name="asm-var"></a>Calling variants from assembly-to-reference alignment
+```sh
+# don't forget the "--cs" option; otherwise it doesn't work
+minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa \
+  | sort -k6,6 -k8,8n \
+  | paftools.js call - > out.txt
+```
+The first few lines in `out.txt` are
+```
+R       NC_000913       0       257899
+V       NC_000913       668     669     1       60      g       -       tig00000001     3439623 3439623 +
+V       NC_000913       896     897     1       60      g       -       tig00000001     3439850 3439850 +
+V       NC_000913       1304    1305    1       60      g       -       tig00000001     3440257 3440257 +
+```
+where an `R`-line gives the regions coverged by one contig; a `V`-line consists of:
+
+1. Reference sequence name
+2. Reference start
+3. Reference end (a 0-based, half-close-half-open interval)
+4. Contig coverage (please ignore a `V`-line if this number is not one!)
+5. Mean mapping quality of contigs covering the site
+6. Reference base ("-" for an insertion)
+7. Contig base ("-" for a deletion)
+8. Contig name
+9. Contig start
+10. Contig end
+11. Contig strand
+
+`paftools.js call` does not support VCF output. This feature is planned but has
+not been implemented yet.
+
+
+
+
 ## <a name="read-overlap"></a>Read Overlap
 
 ### <a name="long-read-overlap"></a>Long read overlap
@@ -86,6 +133,8 @@ paftools.js mason2fq tmp.sam | seqtk seq -1 > ecoli_mason_2.fq
 minimap2 -x ava-pb ecoli_p6_25x_canu.fa ecoli_p6_25x_canu.fa > overlap.paf
 # For Nanopore reads (ava-ont also works with PacBio but not as good):
 minimap2 -x ava-ont -r 10000 ecoli_p6_25x_canu.fa ecoli_p6_25x_canu.fa > overlap.paf
+# If you have miniasm installed:
+miniasm -f ecoli_p6_25x_canu.fa overlap.paf > asm.gfa
 ```
 Here we explicitly applied `-r 10000`. We are considering to set this as the
 default for the `ava-ont` mode as this seems to improve the contiguity for
@@ -120,3 +169,4 @@ minimap2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam
 
 [pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
 [mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2
+[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md