This assemblies of HG004 from ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter may be downloaded from ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/BCGSC_HG004_ABySS2.0_assemblies_12082016/.
The preprint is archived on bioRxiv: http://dx.doi.org/10.1101/068338.
We downloaded the Illumina WGS 2x250 bp paired-end sequencing data and the Illumina 6 kbp mate-pair sequencing data of the Ashkenazi mother (HG004). We removed adapters from the mate-pair reads using NxTrim 0.4.0. We corrected sequencing errors in the reads using the tool BFC. The data is downloaded from https://github.com/genome-in-a-bottle/giab_data_indexes.
We assembled this data using
- ABySS 1.9.0
- ABySS 2.0.0 (branch bloom-abyss-preview)
- BCALM2 2.0.0
- DISCOVARdenovo 52488
- MEGAHIT 1.0.6
- Minia 3.0.0-alpha1
- SGA 0.10.14
- SOAPdenovo 2.04
For the assembly scripts, see the Makefile in https://github.com/sjackman/giab.