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A healthy taste of resources available, specifically for this course - not a comprehensive catalog.

Linux

Community Resources

Sequencing Technologies

FASTQ analysis/manipulation/QC

Reference genomes

Basic alignment and aligners

  • Comparison of different aligners
    • by Heng Li, developer of bwa, samtools, and many other bioinformatics tools
  • File formats
    • input: FASTQ format
    • output: the SAM (Sequence Alignment Map) format specification (SAM1.pdf)
  • Aligners
  • The BioITeam has some TACC-aware alignment scripts you might find useful:
    • bwa alignment
      • /work/projects/BioITeam/common/script/align_bwa_illumina.sh
    • bowtie2 alignment
      • /work/projects/BioITeam/common/script/align_bowtie2_illumina.sh
    • merging sorted BAM files (read-group aware)
      • /work/projects/BioITeam/common/script/merge_sorted_bams.sh
    • email or come talk to Anna if you have questions or problems

Transcriptome-aware aligners

Alignment analysis

File formats and conversion

UCSC Genome Browser

RNAseq/Transcriptome analysis

Variant calling

Genome Annotation



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