DATA PRESENTED IN: 

Rene L Warren; Chen Yang; Benjamin P Vandervalk; Bahar Behsaz; Albert Lagman; Steven JM Jones; Inanc Birol (2015)
LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. GigaScience. 
DOI: 10.1186/s13742-015-0076-3

To re-run LINKS assemblies on genomes <=12 Mbp, simply run (./runall.sh) at the unix shell.  Make sure you have sufficient RAM on your machine before you do so. The LINKS distribution also includes these shell scripts in the ./test folder.

runall.sh will run the following scripts:

./runme_EcoliK12single.sh
final LINKS assembly/output (re-scaffolded from contigs): ecoliK12-ONT_linksSingleIterationTIG.*
final LINKS assembly/output (re-scaffolded from scaffolds): ecoliK12-ONT_linksSingleIterationSCAFF.*

./runme_StyphiH58iterative.sh
final LINKS assembly/output: STH58links11.*

./runme_EcoliK12iterative.sh
final LINKS assembly/output (full 2D R7): K12links30.*

./runme_EcoliK12iterativeRAW.sh
final LINKS assembly/output (raw R7.3): RK12links30.*

./runme_EcoliK12iterativeA2D.sh
final LINKS assembly/output (all 2D R7): AK12links30.*

./runme_ScerevisiaeS288citerative.sh
final LINKS assembly/output: S288clinks29.*

./runme_ScerevisiaeS288citerativeNanocorr.sh
final LINKS assembly/output: S288cNANOlinks40.*

./runme_ScerevisiaeW303iterative.sh
final LINKS assembly/output: W303links27.*

./runme_ScerevisiaeW303iterativeNanocorr.sh
final LINKS assembly/output: W303NANOlinks29.

For larger genomes (A. thaliana and P. glauca), we provide the shell recipes (parameters) and final re-scaffolded assemblies:

A. thaliana (120 Mbp genome)
===========================
Ler-1 Allpaths-LG assemblies of Illumina reads, LINKS re-scaffolded with:
ECTools-corrected Pacbio reads : LINKSrecipe_athaliana_ectools.sh
final LINKS assemblies/output:ecapATlinks4.*
Raw Pacbio reads : LINKSrecipe_athaliana_raw.sh
final LINKS assemblies/output: rawapATlinks4.*

Illumina assembly (Schatz lab http://schatzlab.cshl.edu/data/ectools/), LINKS
re-scaffolded with RAW or ECTools-corrected Pacbio reads:
LINKSrecipe_athaliana_illumina_raw-or-ect.sh
final LINKS assemblies/output:
RAW: rawillATlinks4.*
ECTools: ecillATlinks4.*

P. glauca (white spruce, PG29, 20 Gbp genome)
Illumina assembly of PG29 re-scaffolded with WS77111 genotype:
LINKSrecipe_pglaucaPG29-WS77111.sh
final LINKS assembly/output: whiteSpruceLINKS14.*