1632 days ago
ngs-bits - Short-read sequencing tools
Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows1629 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 a...A file containing a high continuity assembly and a BAM file with all available reads m...1629 days ago
Kevler: Reference-free variant discovery in large eukaryotic genomes
Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's...1618 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads....1618 days ago
MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are as accura...1618 days ago
vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt1618 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments.&nb...1618 days ago
Understanding your reads and mapping !
One of the best tutorial for beginners ... https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html1617 days ago
HASLR: a tool for rapid genome assembly of long sequencing reads
HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (s...xford Nanopore) together with Next Generation Sequencing reads (...1615 days ago