### Cimex lectularius genome - 1.1 ###

This is a reassembly of the original, unanchored C. lectularius genome (Genbank accession: PRJNA167477) into autosomal linkage groups based on a linkage map produced by Fountain et al (2016; G3 in press). The 14 linkage groups consist of 74 anchored scaffolds from the previous assembly and in total account for 433 Mb or 67% of the genome.

The linkage map was assembled using SNP calls derived from RAD-seq analysis of a F2 cross between strains resistant and susceptible to pyrethroid insecticides. RADs were mapped to the original reference, SNPs called using the Stacks pipeline and linkage map construction performed using R/qtl.

Reassembly using the linkage map was performed in Chromonomer 1.03 (http://catchenlab.life.illinois.edu/chromonome) using default settings.
 
Scripts for mapping, SNP calling and linkage map estimation can be found here: http://dx.doi.org/10.5061/dryad.d4r50

Files are:

### Clec_1.1_genome.agp ###

AGP with a definition of the reassembly; contains linkage groups and scaffold anchoring positions

### Clec_1.1_integrated.fa ### 

Fasta file of genome reassembled into linkage groups; also contains unplaced scaffolds

### Clec_1.1_scaffolds.agp ### 

AGP but defined at the scaffold level and not with linkage groups. Also contains scaffold split positions.

### Clec_1.1_split_scaffold_map.tsv ### 

List of split scaffolds and split coordinates.

### Clec_1.1_unplaced_scaffolds.agp ### 

AGP of unmodified, unplaceable scaffolds.

### Clecl_1.1_summary.log ### 

Log from chromonomer run. Details scaffold splits, anchoring positions and linkage group lengths.