Jit
Enthusiast computational biologist with business dream !!!
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gSearch: a fast and flexible general search tool for whole-genome sequencing
By Jit 2868 days agoml.ssu.ac.kr - gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2832 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...sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
By Jit 2769 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLmosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2404 days agogithub.com - 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...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 2325 days agogithub.com - 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...
