Glossary

Accno –– Accession number of the input read. If this is a Paired End read, the accno is followed by an underscore character and the mention “left” of “right”, for which half of the pair this read comes from.

Assembly – computation performed by the GS .De Novo Assembler. See GS De Novo Assembler.

cDNA Project – a project that contains cDNA data. See Project.

Command Line Interface (CLI) – software commands run fro the command line prompt.

Contig Graph – description of branching structure between contigs.

Flowgram – series of values representing the results of a 454 Sequencing run. Provides the input data for the GS De Novo Assembler and the GS Reference Mapper.

fna file – Phred-equivalent file that contains the nucleotide sequences of all of the contigs and associated nucleotide Quality Scores.

GS De Novo Assembler – application that Identifies pairwise overlaps between reads, constructs multiple alignments of overlapping reads, and divides or introduces breaks into the multiple alignments in regions where consistent differences are found between different sets of reads. (This step results in a preliminary set of “contigs” that represent the assembled reads.) After attempting to resolve branching structures between contigs, the software generates consensus basecalls of the contigs by using quality and flow signal information for each nucleotide flow included in the contigs’ multiple alignments. Output includes the contig consensus sequences and corresponding quality scores, and an ACE file of the multiple alignments and assembly metrics files.

GS Reference Mapper – software that aligns sequencing reads against reference sequences (consisting of one or more sequences or a GoldenPath genome), with or without associated annotations. Mapping generates consensus sequences of the reads that align against the reference and also computes statistics for variations found in the reads, relative to the reference.

Genomic Project – a project that contains genomic assembly data.

GS Reads – result of the sequencing process that provides input to an assembly project. Read types can be paired-end or non-Paired end. The Read Type Specification auto-detects unknown read type data.

HC Diffs – High Confidence difference. The GS Reference Mapper application uses a combination of flow signal information, quality score information and difference type information to determine if a difference is High-Confidence.

Isogroup – represents the Transcriptome Assembler groups of contigs whose branches could not be resolved.

Isotig – .

Multiplex Identifier (MID) – a unique identifier that is attached a DNA library to identify the library to which an individual read belongs. Allows multiple libraries tagged with different MIDs to be sequenced together, within an individual PTP Device.

Newbler – software package for De Novo DNA sequence assembly that is run by the GS Assembler graphical user interface or the Command Line Interface (CLI).

Path extension – in transcriptome assembly, an isotig path that starts at an initiating contig and continues until a terminating condition is found.

Path termination – in transcriptome assembly, represents the end of an isotig.

Path traversal – in transcriptome assembly, analysis of branching of contigs in an isogroup.

Project – provides an interface for creating, modifying, and running assemblies using the GS De Novo Assembler. The project folder in the file system contains the assembly project files. Users can run projects from the command line interface or using a graphical user interface (GUI).

Qual file - Phred-equivalent file that contains the nucleotide sequences of all of the contigs and associated nucleotide Quality Scores

Read Status - – status of the read in the assembly, which can be: Assembled, PartiallyAssembled, Singleton, Repeat, Outlier or Too Short.

Rearrangement Points – A single structural variation relative to the reference sequence.

Rearrangement Regions –When a cluster of paired-end reads that are considered False Pairs shows a consistent deviation from the reference (varying either in size or expected orientation), a rearrangement region is reported.

Reference Data – Data files that contain reference DNA sequences for comparison to flowgrams.

Scaffolds – a series of contigs that are in the right order but not necessarily connected in one continuous stretch of sequence. The GS De Novo Assembler uses Paired End information calculate the approximate the distance between the contigs.

SFF File – Standard Flowgram Format file - output data from the 454 Genome Sequencer system.

SFF Tools – Software tools for managing SFF files.

Structural Variations – larger-scale changes relative to the reference that are indicated by a group of reads. Entries in the table are classified as either Rearrangement points or Rearrangement regions.