naturalis / de-novo-assembly

Contains shell scripts with example usage of NGS assembly tools for mid-size (insect) genomes.

de-novo-assembly

Contains shell scripts with example usage of NGS de novo assembly tools for mid-size (insect) genomes.

• conf - configuration files for assembly tools
• doc - project documentation
• ref - background reference materials
• results - test data assemblies
• src - shell scripts to run assemblies and code for subsampling

Data

The data used to develop this project were short reads of two phytophagous insect species (Rhagoletis cerasi and Gonioctena quinquepunctata) for which, respectively, three and two individuals were sequenced on the Illumina platform. The data for each species are pooled to obtain a composite assembly, (which will subsequently be used as a reference against which the individuals are mapped in order to identify regions that vary between host plant races).

Rhagoletis cerasi, individual 1, host plant 1

• C0A7AACXX_101851-02_TGACCA_L001_R1.fastq.gz
• C0A7AACXX_101851-02_TGACCA_L001_R2.fastq.gz
• C0A7AACXX_101851-02_TGACCA_L002_R1.fastq.gz
• C0A7AACXX_101851-02_TGACCA_L002_R2.fastq.gz
• D0TRBACXX_101851-02_TGACCA_L004_R1.fastq.gz
• D0TRBACXX_101851-02_TGACCA_L004_R2.fastq.gz

Rhagoletis cerasi, individual 2, host plant 1

• C0A7AACXX_101851-03_ACAGTG_L001_R1.fastq.gz
• C0A7AACXX_101851-03_ACAGTG_L001_R2.fastq.gz
• C0A7AACXX_101851-03_ACAGTG_L002_R1.fastq.gz
• C0A7AACXX_101851-03_ACAGTG_L002_R2.fastq.gz
• D0TRBACXX_101851-03_ACAGTG_L004_R1.fastq.gz
• D0TRBACXX_101851-03_ACAGTG_L004_R2.fastq.gz

Rhagoletis cerasi, individual 3, host plant 2

• C0A7AACXX_101851-06_GCCAAT_L001_R1.fastq.gz
• C0A7AACXX_101851-06_GCCAAT_L001_R2.fastq.gz
• C0A7AACXX_101851-06_GCCAAT_L002_R1.fastq.gz
• C0A7AACXX_101851-06_GCCAAT_L002_R2.fastq.gz
• D0TRBACXX_101851-06_GCCAAT_L004_R1.fastq.gz
• D0TRBACXX_101851-06_GCCAAT_L004_R2.fastq.gz

Gonioctena quinquepunctata, individual 1, host plant 1

• C0A7AACXX_101851-07_CAGATC_L001_R1.fastq.gz
• C0A7AACXX_101851-07_CAGATC_L001_R2.fastq.gz
• C0A7AACXX_101851-07_CAGATC_L002_R1.fastq.gz
• C0A7AACXX_101851-07_CAGATC_L002_R2.fastq.gz
• D0TRBACXX_101851-07_CAGATC_L004_R1.fastq.gz
• D0TRBACXX_101851-07_CAGATC_L004_R2.fastq.gz

Gonioctena quinquepunctata, individual 2, host plant 2

• C0A7AACXX_101851-10_CTTGTA_L001_R1.fastq.gz
• C0A7AACXX_101851-10_CTTGTA_L001_R2.fastq.gz
• C0A7AACXX_101851-10_CTTGTA_L002_R1.fastq.gz
• C0A7AACXX_101851-10_CTTGTA_L002_R2.fastq.gz
• D0TRBACXX_101851-10_CTTGTA_L004_R1.fastq.gz
• D0TRBACXX_101851-10_CTTGTA_L004_R2.fastq.gz

de-novo-assembly's Issues

subsampling? config files? shell scripts?

Het is een goed idee om zo vroeg mogelijk (=nu of gisteren) te beginnen met het opslaan van scripts voor data sampling, shell scripts voor het runnen van tools en de config files voor de tools. Github is niet bedoeld als eindstation maar als tussentijdse "undo" voor als er een rampje gebeurt. Gebruik het dus hiervoor.

SOAP de novo resultaten

Wellicht kunnen de *.log en *.err bestanden van de twee soorten toegevoegd worden?

Clean up Dwin's output