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a simple tool for in-silico PacBio and Oxford Nanopore read generation

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pblibsim

#####Update 5/12/2016: Construction of a new, packaged version is underway (v1)!.

#####Update 1/8/2016: This repo is under construction. I'll be pushing some usable updates soon, but they may require some adaptation to your configutations. Working on a more generalized version for the near future.


Here's a general pipeline for this code.

  1. Get a reference genome/assembly by chromosome (ie. chr1.fa, chr2.fa,)
  2. Generate a distribution of chromosome lengths (generate_chrdist.py)
  3. simulation.py (many parameters still must be hard-coded in this draft version.) This generates a BED file of simulated reads.
  4. sortBed.sh - sorts BED files by chromosome.
  5. getFasta.sh - requires BEDTools, generates simulated FASTA files. This is written to be easily parallelizable.
  6. (Optional, but used in AGBT presentation) countSimDimers.sh

This is a draft version of pblibsim. Your mileage may vary.

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a simple tool for in-silico PacBio and Oxford Nanopore read generation

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