Jit
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FiNGS: Filters for Next Generation Sequencing
By Neel 1364 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...
Libraries or management tools for high throughput sequencing data
Last updated 49 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2240 days agogithub.com - VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2060 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Jit 1764 days agogithub.com - 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...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2187 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2283 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 2549 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2356 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish...
By Jit 2130 days agogithub.com - Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...
