Jit
Enthusiast computational biologist with business dream !!!
Our Sponsors
Related items
AMStat: display statistics of large sequence files from next generation sequencing projects
By Neel 2826 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...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2771 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2457 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...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 2363 days agogithub.com - 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,...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1623 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...
Single Cell RNAseq data analysis tutorial !!
Last updated 3173 days ago by Robert M WilliomsA major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the average expression level for each gene across a large population of input cells Useful for comparative transcriptomics,...KisSplice
By Jit 3642 days agokissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...YASRA: Reference based assembler
By Abhimanyu Singh 3445 days agogithub.com - YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a...Tadpole: an assembler, error-corrector, and read-extender
By BioStar 2374 days agojgi.doe.gov - Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and therefore, is not particularly good for diploid organisms. Tadpole is...coursera genome assembly tutorial
By Jit 3176 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)
