Credit Samtools

Author: charles-plessy

CITATIONS.md

@@ -26,6 +26,10 @@
 
   > Frith MC, Shaw J, Spouge JL. How to optimally sample a sequence for rapid analysis. doi: 10.1093/bioinformatics/btad057 PubMed PMID: 36702468 (Describes the lastdb -u RY sparsity options.)
 
+- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
+
+  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

README.md

@@ -29,6 +29,7 @@ The main steps of the pipeline are:
 2. Genome indexing ([`lastdb`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst)).
 3. Genome pairwise alignments ([`lastal`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastal.rst)).
 4. Alignment plotting ([`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst)).
+5. Alignment export to various formats with [`maf-convert`](https://gitlab.com/mcfrith/last/-/blob/main/doc/maf-convert.rst), plus [`Samtools`](https://www.htslib.org/) for SAM/BAM/CRAM.
 
 The pipeline can generate four kinds of outputs, called _many-to-many_, _many-to-one_, _one-to-many_ and _one-to-one_, depending on whether sequences of one genome are allowed match the other genome multiple times or not.