Lists (3)
Stars
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
A single molecule sequence assembler for genomes large and small.
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Structural variant and indel caller for mapped sequencing data
C++ API & command-line toolkit for working with BAM data
Toolset for SV simulation, comparison and filtering
Strelka2 germline and somatic small variant caller
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…
Structural variation and indel detection by local assembly
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
Kraken taxonomic sequence classification system
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It u…
Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
microsatellite instability detection using tumor only or paired tumor-normal data
Genetic multiplexing of barcoded single cell RNA-seq