Tomo Kurobe Research Website


Bioinformatics

Here are useful links for bioinformatics analysis


Web-Based Programs


Collection of Useful Scripts


BLAST Search


Standalone BLAST and Related Commands


MAFFT


Sequence Analysis Scripts (Suggested Work Flow for NGS_Part I)

  1. Unwrap fasta sequences
    • cat R1tag.fasta | awk '/^>/{print s? s"\n"$0:$0;s="";next}{s=s sprintf("%s",$0)}END{if(s)print s}' > R1tag_noLineBleak.fasta
    • fasta_formatter [-i INFILE] [-o OUTFILE] [-w N (select "0" for removing line break) [-t (tabular output)]] [HannonLab FASTX-Toolkit]
  2. Sorting sequences by barcode sequences
    • cat R1_001tag_noLineBreak.fasta | fastx_barcode_splitter.pl -bcfile barcodes_DS_SB.txt --bol --exact --prefix /home/tehbioinfo/Users/tomo/NGS_Data_Analysis/
  3. Trim fist 6 base pairs (barcode)
    • fastx_trimmer -i DS.fasta -f 7 -o DS_trimmed.fasta
    • fastx_trimmer -i SB.fasta -f 7 -o SB_trimmed.fasta

Sequence Analysis Tools


RNA seq

Metagenomics Analysis

Tutorials

iPlant

Databases


Service Lab