LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring...f base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncer...1566 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 201...eraldine Van der Auwera PDF Video 03/19/15 Mapping, processing, and duplicate ma...ard tools Matt Sooknah PDF Video 03/19/15 Mapping and processing RNAseq Ami Le...1562 days ago
1535 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the tax...tagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the...1476 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
SqueezeMeta is a full automatic pipeline for metagenomic...haracteristics: Co-assembly procedure with read mapping for estimation of the abundan...otential chimeras. Metatranscriptomic support via mapping of cDNA reads against referen...1385 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant...1311 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE...king single TF, 2) Breast tumors divided along PAM50 designations 3) Whole brain s...1284 days ago
CoverM: Read coverage calculator for metagenomics
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relativ...ndividual contigs coverm contig (help). Calculating coverage by read mapping, its input can either be BAM...1129 days ago
Kmer: a suite of tools for DNA sequence analysis
More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparision tool: Comparative mapping between two genome assemblies...1019 days ago
990 days ago