The Sino-Danish Pig Genome Project

Genomic sequences

Reference

Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
Rasmus Wernersson, Mikkel H Schierup, Frank G Jorgensen, Jan Gorodkin, Frank Panitz, Hans-Henrik Staerfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshoj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane K-S Wong, Jun Yu, Jian Wang, Christian Bendixen, Merete Fredholm, Soren Brunak, Huanming Yang, Lars Bolund
BMC Genomics 2005, 6:70 (10 May 2005)

Raw data - trace files

All genomic reads from the shutgun sequencing (3.8 million of length 100bp and above) has been submitted to the NCBI Trace Archive. The files are found under the center name "SDJVP" [ SDJVP status page]. The total size of the submitted trace file archives is appx. 400 gigabytes.

Processed data - FASTA files

As a service to people who are interested in working with the genomic sequences, but who are not interested in working on the large data set of the original trace files, we have extracted the sequence information to a set of FASTA format files. These files are hosted at the Center for Biological Sequence Analysis at the Technical University of Denmark.

Please refer to the publication for information about how the trace files were processed.

Sequence count	Description	File size	File link	MD5 checksum
4.168.869	All sequences - no cutoff	2.5gb	pigdb_genomic_all_screen.fsa	6fc05ba22387e5f20e3b4dc9a01657b1
		681mb	pigdb_genomic_all_screen.fsa.gz	b641a0130ad298bddb136dbc1ca2e78b
		613mb	pigdb_genomic_all_screen.fsa.bz2	8878c9a37585b526b9613b29ea8cf2fb
3.881.997	Min length 100bp. Max 40% X. Leading and trailing X'es removed.	2.6gb	pigdb_genomic_all_screen.minlen100_max40%X.fsa	836aefd1c8bb63f756b12daa1f953c8d
		662mb	pigdb_genomic_all_screen.minlen100_max40%X.fsa.gz	5068b974f4af8a59eac9191b9121c05c
		592mb	pigdb_genomic_all_screen.minlen100_max40%X.fsa.bz2	4d0cbdab3b0cbe664e650167b26062a3
3.881.805	Min length 100bp. Max 20% X. Leading and trailing X'es removed.	2.6gb	pigdb_genomic_all_screen.minlen100_max20%X.fsa	fa38e1dcde4874788bbbe86ec13b2367
		662mb	pigdb_genomic_all_screen.minlen100_max20%X.fsa.gz	8eaa91405af7dd5d9e59abafae0cc694
		592mb	pigdb_genomic_all_screen.minlen100_max20%X.fsa.bz2	42ea516729bf048664651941807f9f59
3.693.393	Min length 200bp. Max 40% X. Leading and trailing X'es removed.	2.5gb	pigdb_genomic_all_screen.minlen200_max40%X.fsa	dc4710d6aabefc8f204455650d2416fe
		650mb	pigdb_genomic_all_screen.minlen200_max40%X.fsa.gz	eb5d5f313a3a054a1356e53069d23e4b
		583mb	pigdb_genomic_all_screen.minlen200_max40%X.fsa.bz2	a73039ab9a4f9e514f80dabda486250c
3.693.345	Min length 200bp. Max 20% X. Leading and trailing X'es removed.	2.5gb	pigdb_genomic_all_screen.minlen200_max20%X.fsa	19614bb143c9465cd9193bfd16896ada
		650mb	pigdb_genomic_all_screen.minlen200_max20%X.fsa.gz	8e3520ed0f5b92ada8708b57145694d0
		583mb	pigdb_genomic_all_screen.minlen200_max20%X.fsa.bz2	cf3d4f1c1c1aaf710ecd3c7f611e7baa

[Browse data directory]

Contact: Rasmus Wernersson.