Table 1.
Software and databases used in this work.
| Tool or resource name | Version | Reference | Source website | Additional parameters used | Comments |
|---|---|---|---|---|---|
| Data QC/filtering | |||||
| fastq-mcf | 1.04.636 | Aronesty (2011) | http://code.google.com/p/ea-utils/wiki/FastqMcf | ||
| Preliminary assembly and read mapping | |||||
| ABySS | 1.3.6 | Simpson etal. (2009) | http://www.bcgsc.ca/platform/bioinfo/software/abyss | k-mer of 61 | The user might care to change the k-mer value depending on the quality and length of their read data; it is not necessary to optimize this value. The program can also be run treating any paired (mate or paired-end) data as single-end. |
| Bowtie 2 | 2.1.0 | Langmead and Salzberg (2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | -k 1 –very-fast-local | The settings used are designed to map reads uniquely and quickly |
| Taxonomic annotation | |||||
| BLAST+ | 2.2.28 | Ye et al., 2006; Johnson et al., 2008 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download | -task megablast -evalue 1e-5 -max_target_seqs 1 -outfmt ‘6 qseqid staxids’ | |
| NCBI nt | March 1, 2013 | ftp://ftp.ncbi.nlm.nih.gov/blast/db/ | See http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide for definition; one can also use custom databases, or other normalized databases | ||
| TAGC plot scripts | |||||
| gc_cov_annotate.pl | 1.0 | This work | https://github.com/blaxterlab/blobology | ||
| makeblobplot.R | 1.0 | This work | https://github.com/blaxterlab/blobology | 0.01 taxlevel_order | 0.01 is the threshold of displaying annotated contigs, and taxlevel_order sets the taxon level to display |
| ggplot2 | Wickham (2009) | http://ggplot2.org/ | |||
| NCBI taxonomy heirarchy files | March 2013 | ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz | |||
| Blobsplorer | |||||
| JQuery | 1.8.2 | http://jquery.com/ | http://code.jquery.com/jquery-1.8.2.js | Additional JQuery plugins used: jquery-ui, dropkick, tagsinput, placeholder, chardin.js | |
| Raphael | 2.1.0 | http://raphaeljs.com/ | http://github.com/DmitryBaranovskiy/raphael/raw/master/raphael-min.js | additional Raphael plugins used: raphael.export | |
| Assembly validation | |||||
| Caenorhabditis briggsae proteome | WS230 | Stein etal. (2003) | ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/sequence/protein/ | See http://www.wormbase.org/species/c_briggsae#02–10 | |
| Caenorhabditis sp. 5 EST assembly | NEMBASE4 | Elsworth etal. (2011) | http://www.nematodes.org/downloads/databases/NEMBASE4/CSC_nuc.fsa | See http://www.nematodes.org/nembase4/species_info.php?species=CSC | |
| Caenorhabditis sp. 5 RNA-Seq transcriptome assembly | 1.0 | http://nematodes.org/genomes/caenorhabditis_sp5/index.html | Unpublished data from the Caenorhabditis sp. 5 genome project | ||
| CEGMA | 2.4 | Parra etal. (2007) | http://korflab.ucdavis.edu/datasets/cegma/ | ||