Jit
Enthusiast computational biologist with business dream !!!
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nanofilt: Filtering and trimming of long read sequencing data
By Jit 2929 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...AMStat: display statistics of large sequence files from next generation sequencing projects
By Neel 2827 days agosamstat.sourceforge.net - SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2886 days agoqualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2682 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 2386 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...karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 3107 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 3031 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2385 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 2001 days agogithub.com - Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz...EyeChrom: Visualizing Chromosome Count Data From Plants
By Jit 2767 days agoeyechrom.com - It's goal is to show chromosmal data per genus. Select the genus, and the plot will show the records found for it in the Chromosome Counts Database. note: Report an issue via Gihub: github.com/roszenil/CCDBcurator and...
