Tod Stuber's miscellaneous and experimental scripts

alignmentreport-latex.sh Alignment and run LaTeX summary report as pdf. Working directory must contain reference with .fasta extension and single or paired FASTQ reads. Kraken can be called with -k option.

assemble_verify.sh Select assemble program, verify reads against local BLAST NT database and run Kraken. Run with -h option for help.

assemblereport-latex.sh Assemble and run LaTeX summary report as pdf

blast-contigs.sh Give fasta file as argument. Get a quick summary of read identifications against NT database.

Bruc_MLST.sh Get Brucella species MLST type.

highqualitymaker.sh Make a HQ VCF for GATK best practices.

krakenreadfinder.sh Pull reads based on Kraken identifications. Pull reads by either identification name or report line number. See script header for details.

ksnp_validate.sh For a specified node get SNP positions and annotation.

ksnp3_run.sh Run kSNP3 on working directory containing draft or finished assembled genomes. Run with -h option for help.

makeReference.sh Make a reference from a reference guided assembly mimicking idvirus script.

ncbi_download_assembled_genomes_from_xml.sh Quickly select WGS from NCBI in XML format and download.

oligo_identifier_test.sh Count oligos in raw FASTQ files. Used for primer/probe design.

packagefastqs.sh Package FASTQs into directories and echo one-liner to call on all directories.

quickalignment.sh Working directory to have paired FASTQs and reference with .fasta extension.

readfindingbyends.sh Gather reads from alignment/assembly and gather additional reads by pair read information.

sixteen_s.sh 16s and rpoB analysis and report. Run without arguments for help.

sra_download.sh Download SRA using DNA Nexus urls.