Jit
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AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
By BioStar 2530 days agosourceforge.net - AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2412 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...HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 2386 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2280 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2152 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 1838 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 1744 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,...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 1382 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...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 2728 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2289 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...
