jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants...ms. It can either read reference genomes from FASTA files or simulate new ones. Genomic...statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations&m...1758 days ago
GffCompare: Program for processing GTF/GFF files
The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).1775 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene se...1669 days ago
Bioinformatics web development course
This web development course, targeted at Biology and Bioinformatics students, aims...rrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-c...1654 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X geno...ven a window size--as would be used for CNV calling.the mean per-region given a BED f...1644 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effective and ve...lso very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs ...1628 days ago
MGSE: Mapping-based Genome Size Estimation
MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM fi...1583 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for...1576 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Rcorrector has an accuracy higher than or comparable to existing methods, inc.../. Usage: perl run_rcorrector.pl [OPTIONS] OPTIONS: Required -s seq_files: comma separated files for single-end data sets -1...1564 days ago
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