1625 days ago
MGSE: Mapping-based Genome Size Estimation
MGSE can harness the power of files generated in genome sequencing projec...he genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapp...f a COV file based on the (sorted) BAM file (also possible via MGSE direc...1599 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
...ased toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search fo...sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome vi...1592 days ago
1590 days ago
Nucleus: Python and C++ code for reading and writing genomics data.
...igned to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In...n with the TensorFlow machine learning framework, as anywhere a genomics file is consumed or produced, a Te...1582 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...ge: perl run_rcorrector.pl [OPTIONS] OPTIONS: Required -s seq_files: comma separated files for single-end data sets -...n bloom filter; 2-start from dumping kmer counts into a jf_dump file; 3-start from error correc...1580 days ago
1577 days ago
SeqMule: Automated human exome/genome variants detection
SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.1567 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad...1563 days ago
tinycov: standalone command line utility written in python to plot coverage from a BAM file
Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plot...1533 days ago