Commit 83b592f3 authored by peguerin's avatar peguerin
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readme update

parent 6a4acd4b
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#### Katharina Fietz, Pierre-Edouard Guerin, Elena Trofimenko1, Véronique Arnal, Montserrat Torres-Oliva, Stéphane Lobréaux, Angel Pérez-Ruzafa, Stephanie Manel, Oscar Puebla
Montpellier, 2017-2019
2017-2019
Submited to Molecular Ecology Ressources, 2019
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## Nuclear Genomes assembly
Nuclear genomes were assembled using the Platanus assembler (Kajitani et al., 2014). Platanus was selected due to its excellent performance with highly heterozygous genomes (Kajitani et al., 2014), as well as with simulated datasets that we produced (data not shown). The paired-end libraries were used to assemble reads into contigs, and both the paired-end and mate-pair libraries were used for scaffolding and gap closing.
Nuclear genomes were assembled using the Platanus assembler. Platanus was selected due to its excellent performance with highly heterozygous genomes. The paired-end libraries were used to assemble reads into contigs, and both the paired-end and mate-pair libraries were used for scaffolding and gap closing.
### Source codes
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## RAD-seq data processing
RA-seq sequences were demultiplexed and filtered using the process_radtags pipeline in STACKS v2.2. Sequences were trimmed to a final length of 139bp due to a drop in read quality towards the end of the read. Taking advantage of paired-end information, clone_filter was used to remove pairs of paired-end reads that match exactly, as the vast majority of these are expected to be PCR clones. Paired-end read sequences were subsequently aligned with BWA to the reference genomes of _M. surmuletus_ and _D. sargus_, and _S. cabrilla_, thereby improving the reliability of stacks building. Aligned reads were sorted using SAMTOOLS 1.9 (H. Li et al., 2009), and loci were built with gstacks providing genotype calls.
RAD-seq sequences were demultiplexed and filtered using the process_radtags pipeline in STACKS v2.2. Sequences were trimmed to a final length of 139bp due to a drop in read quality towards the end of the read. Taking advantage of paired-end information, clone_filter was used to remove pairs of paired-end reads that match exactly, as the vast majority of these are expected to be PCR clones. Paired-end read sequences were subsequently aligned with BWA to the reference genomes of _M. surmuletus_ and _D. sargus_, and _S. cabrilla_, thereby improving the reliability of stacks building. Aligned reads were sorted using SAMTOOLS 1.9, and loci were built with gstacks providing genotype calls.
### Source codes
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