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mansonella_pipeline.md

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Pipeline description and scripts used in Mansonella perstans and Mansonella ozzardi genome project (Sinha et al. 2023)

  • The scripts described here were run on a SGE / Grid Engine via qsub.
  • All required software was installed using conda under various environments.

Authors:

  • Amit Sinha (New England Biolabs, Ipswich, MA, US)

Task 1: Preprocessing of raw reads

Key goals

  • "Clumpify" : remove optical duplicates
  • Removed bad tiles (e.g. in NextSeq data)
  • Trim adapters
  • Remove phiX sequences
  • Remove stretches of poly-G (poly-C on read2) which are an artefact of NextSeq and similar platforms
  • Remove reads from the human host
  • Run FatsQC

Script(s) used :

  • sh.00.preprocess-NextSeq-reads.sh

Task 2: Metagenomic assembly using metaSpades

Key goals

  • Assemble all nematode and potential Wolbachia contigs

Script(s) used :

  • sh.01.metaspades.sh

Task 3: Metagenomic assembly using metaSpades

Assessing genome completeness using BUSCO

Running BUSCO for genome assemblies of Cj and other filarial nematodes

Orthology analysis using OrthoFinder

License

Licensed as GNU General Public License v3.0. See LICENSE file in the root directory of this source tree. License