Team 4 Report: ABySS

ABySS stands for Assembly By Short Sequences.

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

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

• 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

• 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

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.

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

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

• Get parallel versions working
• Finish data analysis (kmergenie, fastqc, etc)
• Do assemblies
• RNA-seq rescaffolding with TransABySS
• Meta-assembly