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Repository ivar_trim
Name: ivar_trim
Owner: iuc
Synopsis: Wrapper for ivar application: ivar trim
iVar is a computational package that contains functions broadly useful for
viral amplicon-based sequencing. Additional tools for metagenomic sequencing
are actively being incorporated into iVar. While each of these functions can
be accomplished using existing tools, iVar contains an intersection of
functionality from multiple tools that are required to call iSNVs and
consensus sequences from viral sequencing data across multiple replicates. We
implemented the following functions in iVar: (1) trimming of primers and
low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and
insertions/deletions, and (4) identifying mismatches to primer sequences and
excluding the corresponding reads from alignment files.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim
Type: unrestricted
Revision: 0:8858fa037a15
This revision can be installed: True
Times cloned / installed: 95

Contents of this repository

Name Description Version Minimum Galaxy Version
Trim reads in aligned BAM 1.0.1+galaxy0 16.01

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis