seqProcessing

Bioinformatic utilities for nucleotide sequences. Written in Bash, perl or python.

Contents

• count_GC_content.py

  Given an input fasta file in single line format and a window size (int), this script will calculate the GC percentage of each region for every non-overlapping window and output it in a bam format
  
  Input: FASTA single line (you can use a preprocessing script like PAGIT's fasta2singleLine.pl)
  Output: bam-like file with the following data - "chromosome startPos endPos GC% "
  Used for: This script was created specifically to use for visualization in Circos software. The input files for this software are required as bam format.
  
  

• extractVariableSites_aln.py

  Finds those positions in a multifasta alignment file that are constant in every sequence, and extracts them, leaving as output only those nucleotides/aminoacids that are variable for at least one of the sequences
  
  Input: MultiFASTA alignment file. Output from any MSA software
  Output: Another multiFASTA file
  Used for: Performing downstream phylogenetic SNP analysis, for example. RAxML, in particular, requires that your input fasta or phy shows only the variable sites if you use the prefix ASC_ in the -m flag (page 27 of this)