Schistosoma mansoni repetitive sequences

For assembly version 3.1 (scaffold level):

• RepBasePerpignanSma31 fasta-file
• RepBasePerpignanSma31 RepeatMasker output as gff-file

For assembly version 5.2 (chromosome level):

• RepBasePerpignanSma52 fasta-file
• RepBasePerpignanSma52 RepeatMasker output as gff-file

Please cite:

Lepesant, J.M., Roquis, D., Emans, R., Cosseau, C., Arancibia, N., Mitta, G. and Grunau, C.: Combination of de novo assembly of massive sequencing reads with classical repeat prediction improves identification of repetitive sequences in Schistosoma mansoni. Exp Parasitol (2012) [PubMed] [ScienceDirect]

Female-specific repeats (more than 99% are on W-chromosome):

• W-specifc-repeats fasta-file
• W-specifc-repeats-31 RepeatMasker output as gff-file for assembly v3.1
• W-specifc-repeats-52 RepeatMasker output as gff-file for assembly v5.2

Please cite:

Lepesant, J.M., Cosseau, C., Boissier, J., Freitag, M., Portela, J., Climent, D., Perrin, C., Zerlotini, A. and Grunau, C.: Chromatin structure changes around satellite repeats on the Schistosoma mansoni female sex chromosome suggest a possible mechanism for sex chromosome emergence. Genome Biol 13 (2012) R14.[PubMed]

SNPs in S. mansoni strains GH2 and Bre:

• SmBre FreeBayes vcf-file
• SmGH2 FreeBayes vcf-file
• SmBre tar.gz archive of mpileup-files by chromosome
• SmGH2 tar.gz archive of mpileup-files by chromosome

Please cite:

Clement, J. A. et al. Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains. PLoS Negl. Trop. Dis. 7, e2591 (2013).[PubMed]

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