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 genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a distribution of proportion of bases covered at or above...Tags: mosdepth, fast, BAM, CRAM, depth, calculation, WGS, exome, target, sequencing
1630 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 WindowsTags: ngs-bits, Short-read, sequencing, tools, ngs
1568 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 mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. MitoZ is available from https://g...Tags: MitoZ, toolkit, animal, mitochondrial, genome, assembly, annotation, visualization, ngs, sequencing
1561 days ago
Tags: DeepVariant, analysis, pipeline, deep, neural, network, genetic, variants, next-generation, DNA, sequencing, data
1560 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. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts t...Tags: FastGT, alignment-free, method, calling, common, SNVs, directly, raw, sequencing, reads, alignment-free
1557 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 (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same s...Tags: HASLR, tool, rapid, genome, assembly, long, sequencing, reads
1554 days ago
iSeqQC: a tool for expression-based quality control in RNA sequencing
iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlat...Tags: iSeqQC, tool, expression-based, quality, control, RNA, sequencing
1538 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to othe...Tags: HASLR, hybrid, assembler, third, generation, sequencing, reads, illumina, pacbio, ont, assembly, genome
1460 days ago
Tags: Parliament2, structural, variant, calls, whole-genome, sequencing, data, NGS
1436 days ago
Tags: McClintock, Meta-pipeline, identify, transposable, element, insertions, next, generation, sequencing, data
1284 days ago