Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: goo...2367 days ago
TULIP - The Uncorrected Long read Itegration Pipeline
...very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short...2357 days ago
IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
...you’re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the fi...2357 days ago
SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
...the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under...2357 days ago
MinION_GC: An R script to do some QC on MinION data
Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt...2347 days ago
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protoco...2345 days ago
jobTree based python wrapper to run the genome simulation tool suite Evolver
...istical summaries of the simulation as it runs including text and image files. Also included are convenienc...and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a comp...2342 days ago
Mugsy: multiple whole genome alignment tool
...regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a refere...2342 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
...a comprehensive alignment-based analysis and generates a set of read profiles serving as the input to the n...given reference genome. NanoSim is written in Python and R. The source files and manual are available at t...2333 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
...ch in SPAdes, in the future we plan to integrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the graph format as SPAdes files. For more details see: Nikol...2322 days ago