README.md

SAGBAC

Semi-Automated Graph-Based Assembly Curator

Dependencies

Please be sure to install the following programs in order to be able to run SAGBAC properly.

• Legacy BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/
• BWA 0.7.17 (or newer version): https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2
• Samtools 1.9 (or newer version): https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
• UCSC utilities: http://hgdownload.soe.ucsc.edu/admin/exe/

Install instructions

• Each assembly should be processed in a newly created directory!
• Clone the SAGBAC repository and rename the SAGBAC directory with a name of your choice.
• Go into the renamed SAGBAC directory

After downloading and installing the software, please be sure to assign the correct commands in the very first lines for the variables "bwa", "samtools", "formatdb", "blastall" in the ISEIS.sh shellscript.

Example data

• Download the assembly data IDBA_assemblies_berS.fasta.gz from figshare (https://doi.org/XXXXXXXX) und gunzip it.
• Create a subfolder in your called example_data and go into it
• Download the SRA accessions XXX with fastq_dump or directly from the NCBI SRA homepage.

Generate initial graph for O. villaricae

• bash SAGBAC.sh "</path/to/work directory>"/IDBA_assemblies_berS.fasta berS "</path/to/work directory>"/example_data/"<SRA_R1.fastq>" "</path/to/work directory>"/example_data/"<SRA_R1.fastq>" initial_graph_berS 3 noChanges 100,3000,1000 1,2,3
• open iGraph_Bert_allLevels_CleanedUp_1_noChanges.pdf which was created in your initial_graph_4Bert directory

Generate final graph for O. villaricae

• Rscript </path/to/work directory>/SAGBAC.R generateGraph </path/to/work directory>/initial_graph_berS/ IDBA_assemblies_berS.fasta.blastout.cutted.tsv berS_illumina-ON-IDBA_assemblies_berS.fasta 49 berS RemoveSmallContigs 0 '854,864,873' '' 1 1.1
• open iGraph_Bert_allLevels_CleanedUp_1_RemoveSmallContigs.pdf which was also created in your initial_graph_4Bert directory

Reorder Blast output

• Rscript "</path/to/work directory>"/SAGBAC.R reorderBlastOutput "</path/to/work directory>"/initial_graph_berS Blastdata4MastercirclePath_Bert_DATE_RemoveSmallContigs.txt newOrder_bertMergePath.csv Bert_illumina-ON-IDBA_assemblies_berS

Generate Master circle

• Rscript "</path/to/work directory>"/SAGBAC.R generateMasterCircle "</path/to/work directory>"/initial_graph_berS Reordered_Blastdata4MastercirclePath_Bert_DATE_RemoveSmallContigs.txt IDBA_assemblies_berS.fasta MasterCircle.fasta "Oenothera villaricae [mitochondrion]"

Predicting PMG isoforms

Rscript "</path/to/work directory>"/SAGBAC.R calculateSubcircles "</path/to/work directory>"/initial_graph_berS graphML_Bert_DATE_RemoveSmallContigs.xml '121,443,518,539,795,773' 2 predictions.pdf

Citation

Please cite the following paper if you used SAGBAC for your data analysis: