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demo

Here is a demo reads.fasta.gz and its config file cfgfile. We can run the demo using the following command.

$ PECAT/build/bin/pecat.pl unzip cfgfile

After a few minutes, the pipeline will generate ./S1/6-polish/racon/primary.fasta and ./S1/6-polish/racon/alternate.fasta.

S.cerevisiae (SK×Y12)

The dataset of S.cerevisiae (SK×Y12) is a pseudo-diploid dataset combining two haploid yeast strains SK1 and Y12. The dataset is available from NCBI at PRJEB7245. The SRA files of SK1 are ERR1080522, ERR1080529, ERR1080536, ERR1080537, ERR1124245 and ERR1140978. The SRA files of Y12 are ERR1080526, ERR1080538, ERR1080539, ERR1140975, ERR1140979, and ERR985361. The config file is configs/cfg_yeast_clr.

A.thaliana (COL×CVI)

The dataset is available from NCBI at PRJNA314706. The SRA files are SRR3405291-SRR3405326. The config file is configs/cfg_arab_clr.

D.melanogaster (ISO1×A4)

The dataset is available from NCBI at PRJNA558397. The SRA file is SRR9969843. The config file is configs/cfg_dro_clr.

B.taurus (Angus×Brahman)

The dataset is available from NCBI at PRJNA432857. The SRA files are SRR6691718,SRR6691728-SRR6691879, SRR6691882-SRR6691900, SRR6691904,SRR6691905,SRR6691908-SRR6691950, SRR6691954-SRR6691960 and SRR6691962-SRR6691984. The config file is configs/cfg_cattle_clr.

A.thaliana (COL×C24)

The dataset is available from NGDC at CRA008108. The config file is configs/cfg_arab_ont.

B.taurus (Bison×Simmental)

The dataset is available from NCBI at PRJNA677946. The SRA files are SRR1310561-SRR13105478. The config file is configs/cfg_cattle_ont.

HG002

The dataset is avaialbe at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/scratch/HG002/sequencing/ont/. The config file is configs/cfg_hg002_ont.