Bioinformatics at COMAV

ngs_backbone

ngs_backbone is a bioinformatic pipeline created to work on Next Generation Sequence (NGS) analysis as well as with sanger sequences. It is capable of cleaning reads, prepare a novo assembly, map reads against a reference, look for SNPs and SSRs, and do some function annotation like: ORFs, GO terms and sequence descriptions.

ngs_backbone:

  • is mainly a wrapper around external tools like: bwa, samtools, blast, etc.
  • uses standard files like fastq, SAM, VCF and GFF to ease the interoperability with other tools.
  • is a command line application.
  • is free software released under the AGPL license with the hope that could be useful to other laboratories.
  • runs in Linux so experience with that operating system is advised when using it.
  • is written in Python.
  • can run in parallel using single node multicore systems and computer clusters.

If you find any problem when running ngs_backbone we’d love to hear from you, so please inform us.

Help

To get help there is a mailing list for ngs_backbone. If you have any question send an email to the list: ngs_backbone@upv.es

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