MaSuRCA 4.0.3

This release adds a new quick-run option for small projects that allows to skip editing a configuration file and specify the data on the command line.
If your project uses data from a single Illumina run that produced either on file of single-end reads or two files for paired end reads, and optionally a single file containing long Nanopore or PacBio reads, you can skip creating a configuration file and use simple command-line interface to run MaSuRCA. The options are described in the usage message that invokes using -h or --help switch. There are three command line switches, -i, -t and -r. -t specifies the number of threads to use, -i specifies the names and paths to Illumina paired end reads files and -r specifies the name and the path to the long reads file. For example:

/path_to_MaSuRCA/bin/masurca -t 32 -i /path_to/pe_R1.fa,/path_to/pe_R2.fa

will run assembly with only Illumina paired end reads from files path_to/pe_R1.fa (forward) and path_to/pe_R2.fa (reverse). An example of the hybrid assembly:

/path_to_MaSuRCA/bin/masurca -t 32 -i /path_to/pe_R1.fa,/path_to/pe_R2.fa -r /path_to/nanopore.fastq.gz

This command will run a hybrid assembly, correcting nanopore reads with Illumina data first. Ilumina paired end reads files must be fastq, can be gzipped, and Nanopore/PacBio data files for the -r option can be fasta or fastq and can be gzipped.