This data resource contains the diversity data set (VCF files) and the functional annotation of SNPs and INDELs for 11 re-sequenced Secale cereale L. lines (five seed lines, five pollen lines and one S. vavilovii line). The analyzed sequence data was produced in the frame of the RYE-Select project. The complete whole-genome shotgun re-sequencing data is archived at the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under the project number PRJEB6215. The discovery of variant positions (VPs) is...

Tool for the removal of paired-end or mate-pair reads from a set of two Illumina FASTQ read files based on read length. Users can specify the minimal length of reads in base pairs that both reads of a pair need to have in order for this read pair to be kept, otherwise the read pair will be removed from the output.

Positions of predicted microRNA precursor loci on the pseudomolecules of barley cv. Morex in GTF format.

This folder contains (i) a tab-separated text file specifying the genomic positions and classifications of repetitive elements and (ii) a README file explaining the contents of the columns in item (i).

A genetic map was constructed from WGS data of 90 Morex x Barke recombinant inbred lines. This TSV file contains the genetic positions (chromosome, centiMorgan coordinate) of all SNP positions defined on the pseudomolecules of barley cv. Morex.

This folder contains a GTF file with the positions of lncRNA loci and a FASTA file with the lncRNA transcripts.

This folder contains the Unix shell (ZSH) and R source code that was used for reading in datasets providing positional information, constructing a BAC overlap graph and a HiC map, and combining this information to derive pseudomolecules sequences. See comments in the source code files for further explanations. Helper functions are provided in the subfolder "functions". Input data sets and processed data are found in the subfolders "data" and "processed_data", respectively.

This table in TSV format defines the composition of the pseudomolecules from BAC sequences and WGS contigs. Moreover, this table provides positional information such as POPSEQ genetic positions and HiC map positions and orientations of BAC overlap clusters as well as the order of BACs within clusters.

Individual BAC assemblies that were considered as input for the construction of the non-redundant sequence for the barley genome. This file contains only a single assembly for each BAC. Each contig/scaffold sequence is printed on a single line without breaks.

This table in TSV format contains positional information of single BAC assemblies such as POPSEQ genetic positions, positions in the physical map and the sequence-based overlap clusters.

A BED file mapping pseudomolecules positions to contig positions in the non-redundant BAC sequence.

A BED file mapping split pseudomolecules positions to contig positions in the non-redundant BAC sequence.

A BED file with coordinates of redundant regions in the pseudomolecule sequence.

A BED file with coordinates of redundant regions in the split pseudomolecule sequence.

A BED file that defines the boundaries at which pseudomolecules were split to make the parts smaller than 512 Mb.

FASTA file with potential contaminant sequence (e.g. vectors, bacterial or phage sequences) that were used to screen barley BAC assemblies.

A genetic map was constructed from genotyping-by-sequencing data of 1,613 recombinant inbred lines of the Morex x Barke population and comprises 2,637 markers. This file contains the genetic positions (chromosome, centiMorgen coordinate). Markers are given as SNP positions in the map-based reference assembly of barley cv. Morex.

A non-redundant sequence was constructed by removing overlaps between neighboring BACs. This FASTA file contains two kinds of sequences: (i) fragments of BAC sequence contigs and (ii) fragments of contigs of the whole-genome shotgun assembly of cv. Morex that harbor high-confidence genes missing from the BAC assemblies. The fragment coordinates are specified in the header line of each fragment (e.g. HVVMRXALLMA0201C17_C2:3198-6633 or morex_contig_95399:1-9263). The coordinates are 1-based (as opposed to 0-based as in the second...

BioNano rawdata were assembled using the BioNano Irysview software. The assembly is provided in CMAP format. Specifications of the CMAP format are available from https://github.com/bionanogenomics/File-Format-Specification-Sheets.

An optical map of the genome of barley cv. Morex was generated by nano-channel electrophoresis using the BioNano Genomic Irys platform. Label positions on single DNA molecules were determined by image analysis and are given in BNX format. Specifications of the BNX format are available from https://github.com/bionanogenomics/File-Format-Specification-Sheets.

A genetic map was constructed from WGS data of 90 Morex x Barke recombinant inbred lines. This TSV file contains the genetic positions (chromosome, centiMorgan coordinate) for all Morex WGS contigs anchored to this map.

FASTA file with pseudomolecule sequences for the seven barley chromosomes and one pseudomolecule composed of unanchored contigs.

FASTA file with pseudomolecule sequences for the seven barley chromosomes and one pseudomolecule composed of unanchored contigs. Residual redundancy affecting 2 - 3 % of the assembled was masked with N characters.

FASTA file with the pseudomolecule sequences of chromosome of 1H to 7H split into two parts each to make the sequence shorter than 512 Mb (at a gap between contigs).

FASTA file with the pseudomolecule sequences of chromosome of 1H to 7H split into two parts each to make the sequence shorter than 512 Mb (at a gap between contigs). Residual redundancy affecting 2 - 3 % of the assembled was masked with N characters.