Ngs tools list

After sequence data has been uploaded and mapped, there are a variety of workflows for NGS analyses that use open-source tools. Any researcher can apply a workflow to his NGS data and retrieve results, without having to interact with a command line.

Additionally, since Galaxy is cloud-based, expensive computing hardware for performing analyses is not needed. In this presentation we will provide an overview of two popular open source RNA-Seq analysis tools, Tophat and Cufflinks, and demonstrate how they can be used in Galaxy. National Center for Biotechnology Information , U. Journal List J Biomol Tech v. Then, the consensus is updated by constructing the consensus only among these sequences.

The match probability of a sequence to a consensus is the sum of the quality values where they do not match equivalent to negative log probability that all mismatches were sequencing errors.

This function does not perform any alignment among consensus sequences. Defaults to the median quality score among all bases in all sequences. Defaults to 0. Defaults to False, which, on ties, selects a single base lexicographically. This option only has an effect when constructing the final consensus sequence as a string, not when calculating error probabilities.

Defaults to False. SequenceError — if any sequence-quality pair have different lengths or number of provided sequences does not match number of provided qualities. Calculate the Levenshtein edit distance between two sequences. SequenceError — When the sequences are unequal lengths.

Dictionary containing SubSequenceParser instances used to parse each group of n sequences. Each key represents a unique subsequence, such as cell barcode, UMI, etc. For internal use only. The expected length for each sequence, based on parsers. None indicates any length is expected. Get a SubSequenceParser by its name. Reorder the file indices according to the reordering list.

This list reorders the file at each index to the value at that index. A new Chemistry instance or the subclass. ChemistryError — If the number sequences does not equal n. The resulting dictionary contains tuple values, where the first element corresponds to the parsed read sequences, while the second corresponds to the parsed quality strings.

Defaults to True. Chemistry Edit on GitHub. This class is used to parse a subsequence out from SubSequenceParser Class that uses a collection of SubSequenceDefinition instances to parse Chemistry Base class to represent a sequencing chemistry.

None if not provided on initialization. False otherwise. Parameters sequences — List of sequences to parse concatenate — Whether or not to concatenate the parsed strings.