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Raw sequence reads: PRJNA493727

posted on 27.11.2018, 03:30 by C. S. Stobie, Michael J. Cunningham, Carel J. Oosthuizen, Paulette Bloomer
This is a link out to the raw RAD data files for both Orange-Vaal yellowfish libraries, batch 2 and batch 3. The files are given as paired-end FastQ files, with _1 referring to Read 1 files and _2 Read 2 files. Read 1 files are associated with the enzyme NlaIII, whereas Read 2 files are the paired reads associated with MluCI. Sequence data was generated by an Illumina HiSeq 2000 for batch 2, and an Illumina HiSeq 4000 for batch 3. The sequencing depth between libraries also differs. Some initial filtering has been performed on these data files by the sequencing company (Beijing Genomics Institute, Hong Kong), however they may require additional filtering as discussed in the paper. FastQ files are in the standard format, with all barcodes and adapters trimmed (apart from any pollution due to overlap). Replicated samples are included in this set of files - for batch 2 this is sample LaO05 which is split into replicates LaO05-1 and LaO05-2 (6 files for each replicate instead of the standard 2). In batch 3 the replicates are 018A3, 029K5, 047K5, and LkA06 where each replicate pair is specified as either -A or -B (two files per replicate, the same as the other unreplicated samples). Sample names match those given in the Supporting Information - please refer to the Supporting Information if you require further information relating to the specimens.




South Africa, Orange River


Labeobarbus aeneus, Labeobarbus kimberleyensis