======Team 4 Report: ABySS======
ABySS stands for Assembly By Short Sequences.

=====Assembler Overview=====

  * Load kmers
  * Find adjacent kmers
  * Generate de Bruijn graphs


=====Workflow=====

  * Generate paths through the reads
  * Merge paths
  * Generate contigs
  * ParseAligns: Empirical fragment-size distribution
      - Maximum Likelihood Estimator
      - Use empirical paired-end size distribution


=====ABySS Details=====

  * Distributes k-mers and deBruijn graph across a cluster
  * Each node announces the list of k-mers it has to nodes that hold their possible extensions
  * 8 bits of storage per k-mer, ACGT forward and reverse extensions
  * Finds paths through contigs that agree with distance estimates and then merge overlapping paths


=====Installing ABySS=====

  * Installation of single processor version was straightforward
  * Difficulty installing parallelized version
  * Developers are active in the community and the assembler has a long history, so documentation is abundant

=====Running ABySS=====
Single processor version: straight forward step
  * Qsub
  * Embedded qsub
  * Exporting paths
  * Abuss-pe [parameters] parallel environment in campusrocks2

Parameters:
Primary
Name: name of assembly
K: size of k-mer
If 1 library of pe data:
In = ‘reads1.fq reads2.fq’
Pipeline organized via makefile: abyss-pe
Autogenerated assembly statistics
Contig, scafold metrics
    * Does not necessarily clean up things that failed.
    * It is better to manually clean the file.

=====Using ABySS, the plan=====

  * Use all libraries, after processing, but no error correction
  * Run the seqprep
  * Run adapter trimming only
  * Run adapter trimming plus merging

====Initial run====
  * The initial run is located on Edser
  * K = 55, arbitrary
  * Did not work

=====For the future=====
  * Get parallel versions working
  * Finish data analysis (kmergenie, fastqc, etc)
  * Do assemblies
  * RNA-seq rescaffolding with TransABySS
  * Meta-assembly