Version 0.2

Author: schellt

README.md

@@ -1,58 +1,70 @@
-# backmap.pl v0.1
+# backmap.pl v0.2
 
 ## Description
-__Automatic short read mapping and genome size estimate from coverage.__
+__Automatic read mapping and genome size estimate from coverage.__
 
-Automatic mapping of paired and unpaired reads to an assembly with `bwa mem`, execution of `qualimap bamqc` and estimation of genome size from mapped nucleotides divided by mode (>0).
-The tools `bwa` and `samtools` need to be in your `$PATH`. The tools `qualimap`, `bedtools` and `Rscript` are optional but needed to create the mapping quality report, coverage histogram and plot of the coverage distribution respectively.
+Automatic mapping of paired, unpaired, PacBio and Nanopore reads to an assembly with `bwa mem` or `minimap2`, execution of `qualimap bamqc` and estimation of genome size from mapped nucleotides divided by mode (>0).
+The tools `samtools`, `bwa` and/or `minimap2` need to be in your `$PATH`. The tools `qualimap`, `multiqc`, `bedtools` and `Rscript` are optional but needed to create the mapping quality report, coverage histogram and plot of the coverage distribution respectively.
 
 ## Dependencies
 
 `backmap.pl` will search for the following executables in your `$PATH`:
 
 Mandatory:
 - [Number::FormatEng](https://metacpan.org/pod/Number::FormatEng)
+- [samtools](https://github.com/samtools/samtools): `samtools`
+
+Short read mapping:
 - [bwa (mem)](https://github.com/lh3/bwa): `bwa`
-- [samtools](https://github.com/samtools/samtools): `samtools` 
+
+Long read mapping:
+- [minimap2](https://github.com/lh3/minimap2): `minimap2`
 
 Optional:
 - [Qaulimap](http://qualimap.bioinfo.cipf.es/): `qualimap`
+- [MultiQC](https://multiqc.info/): `multiqc`
 - [bedtools](https://bedtools.readthedocs.io/en/latest/) `bedtools`
 - [Rscript](https://www.r-project.org/) `Rscript`
 
 ## Usage
 
 ```
 backmap.pl [-a <assembly.fa> {-p <paired_1.fq>,<paired_2.fq> | -u <unpaired.fq>} |
-            -b <mapping.bam>]
+            -pb <pacbio.fq> | -ont <ont.fq> } | -b <mapping.bam>]
 
 Mandatory:
 	-a STR		Assembly were reads should mapped to in fasta format
-	-p STR		Two files with paired reads comma sperated
-			Can be specified multiple times
-	-u STR		One file with unpaired reads
-			Can be specified multiple times
+	AND AT LEAST ONE OF
+	-p STR		Two files with paired Illumina reads comma sperated
+	-u STR		Fastq file with unpaired Illumina reads
+	-pb STR		Fasta or fastq file with PacBio reads
+	-ont STR	Fasta or fastq file with Nanopore reads
 	OR
 	-b STR		Bam file to calculate coverage from
 			Skips read mapping
-			Overrides -nh and -ne
+			Overrides -nh
+			Technologies will recognized correctly if filenames end with
+			.pb(.sort).bam or .ont(.sort).bam for PacBio and Nanopore respectively.
+			Otherwise they are assumed to be from Illumina.
+			
+	All mandatory options except of -a can be specified multiple times
 
 Options: [default]
 	-o STR		Output directory [.]
 			Will be created if not existing
 	-t INT		Number of parallel executed processes [1]
 			Affects bwa mem, samtools sort, qualimap bamqc
-	-pre STR	Prefix of output files [filename of -a or -b]
-	-sort		Sort the bam file (-b) [off]
+	-pre STR	Prefix of output files if -a is used [filename of -a]
+	-sort		Sort the bam file(s) (-b) [off]
 	-nq		Do not run qualimap bamqc [off]
 	-nh		Do not create coverage histogram [off]
 			Implies -ne
 	-ne		Do not estimate genome size [off]
 	-kt		Keep temporary bam files [off]
 	-bo STR		Options passed to bwa [-a -c 10000]
-			Pass options with -bo "<options>"
+	-mo STR		Options passed to minimap [PacBio: -H -x map-pb; ONT: -x map-ont]
 	-qo STR		Options passed to qualimap [none]
-			Pass options with -qo "<options>"
+	Pass options with quotes e.g. -bo "<options>"
 	-v		Print executed commands to STDERR [off]
 	-dry-run	Only print commands to STDERR instead of executing [off]
 
@@ -61,4 +73,4 @@ Options: [default]
 ```
 
 ## Citation
-If you use this tool please cite the dependencies.
+If you use this tool please cite the dependencies as well.