Merge pull request #16 from SAMtoBAM/SAMtoBAM-patch-8-1

Update README.md

Author: SAMtoBAM

README.md

@@ -11,9 +11,10 @@
 **_fusemblr_** is a pipeline wrapper designed for the assembly of complex genomes using nanopore reads and paired-end illumina
 
 **_fusemblr_**  was designed for the <i>Fusarium oxysporum</i> assembly project (hence the name) <br/>
-The pipeline uses Nanopore (the longer and higher coverage the better) and paired-end illumina reads (PacBio is optional) <br/>
+The pipeline only requires Nanopore reads (the longer and higher coverage the better) and an estimation of genome size <br/>
+Paired-end illumina reads and PacBio is optional <br/>
 
-<i>Notably: Providing PacBio Hifi had very little impact on the resulting assemblies using our _Fusarium oxysporum_ datasets as we used recent ONT basecalled data, had high coverage and a good subset of long reads.</i>
+<i>Notably: Providing both illumina PacBio Hifi had very little impact on the resulting assemblies using our _Fusarium oxysporum_ datasets as we used recent ONT basecalled data, had high coverage and a good subset of long reads.</i>
 
 # Easy installation
 
@@ -24,16 +25,16 @@ The pipeline uses Nanopore (the longer and higher coverage the better) and paire
 # How to run
 
 
-	fusemblr.sh -n nanopore.fq.gz -1 illumina.R1.fq.gz -2 illumina.R2.fq.gz -g 70000000
+	fusemblr.sh -n nanopore.fq.gz -g 70000000
 
 	Required inputs:
 	-n | --nanopore		Nanopore long reads used for assembly in fastq or fasta format (*.fastq / *.fq) and can be gzipped (*.gz)
-	-1 | --pair1		Paired end illumina reads in fastq format; first pair. Used for Ratatosk polishing. Can be gzipped (*.gz)
-	-2 | --pair2		Paired end illumina reads in fastq format; second pair. Used for Ratatosk polishing. Can be gzipped (*.gz)	
 	-g | --genomesize	Estimation of genome size, required for downsampling and assembly
 
 	Recommended inputs:
-	-h | --hifi		Pacbio HiFi reads required for assembly polishing with NextPolish2 (Recommended if available)
+	-1 | --pair1		Paired end illumina reads in fastq format; first pair. Used for Ratatosk polishing. Can be gzipped (*.gz)
+	-2 | --pair2		Paired end illumina reads in fastq format; second pair. Used for Ratatosk polishing. Can be gzipped (*.gz)		
+ 	-h | --hifi		Pacbio HiFi reads required for assembly polishing with NextPolish2 (Recommended if available)
 	-t | --threads		Number of threads for tools that accept this option (default: 1)
 
 	Optional parameters:
@@ -51,7 +52,7 @@ The pipeline uses Nanopore (the longer and higher coverage the better) and paire
 # Pipeline in 6 steps: <br/>
 #### 1. Downsampling of reads to a designated coverage using ```Filtlong```
 ###### &nbsp; &nbsp; -default is set to 100X (-x); which provided better assemblies compared to the typical 30-50X 
-#### 2. Polishing of downsampled reads with the paired-end illumina reads using ```Meryl``` and ```Ratatosk correct``` 
+#### 2. Optional: Polishing of downsampled reads with the paired-end illumina reads using ```Ratatosk correct``` 
 ###### &nbsp; &nbsp; -uses a baseline quality score (-Q) of 90 and therefore assumes mildly recent ONT data (e.g. R10 or high-accuracy basecalling)
 #### 3. Genome Assembly
 ##### 3.a. Assembly with```Flye``` 
@@ -74,6 +75,7 @@ The pipeline uses Nanopore (the longer and higher coverage the better) and paire
 
 
 Following assembly it is recommended that you run [PAQman](https://github.com/SAMtoBAM/PAQman) on your resulting assembly to comprehensively check the quality <br/>
+It is recommended to feed your resulting assembly to PAQman alongside the 1.filtlong/*.fz.gz set of reads <br/>
 This can also help you compare any assemblies you have to check for the best.