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CroCo: A program to detect potential cross contaminations in HTS assembled transcriptomes using...
By Jit 2616 days agogitlab.mbb.univ-montp2.fr - CroCo is a program to detect cross contamination events in assembled transcriptomes using sequencing reads to determine the true origin of every transcripts.Such cross contaminations can be expected if several RNA-Seq experiments were prepared...Gooey: Turn (almost) any Python command line program into a full GUI application with one line
By BioStar 2318 days agogithub.com - Turn (almost) any Python command line program into a full GUI application with one line The easiest way to install Gooey is via pip pip install Gooey Alternatively, you can install Gooey by cloning the project to your local directory git...CrossMap: program for genome coordinates conversion between different assemblies
By Rahul Nayak 1502 days ago Comments (1)crossmap.sourceforge.net - CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats...LAST
By Archana Malhotra 3650 days agohttp://last.cbrc.jp/ - LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with...gVolante: Completeness Assessment of Genome/Transcriptome Sequences
By Jit 2404 days agogvolante.riken.jp - gVolante provides an online interface for completeness assessment of user’s original or publicly available sequence datasets as well as for browsing results of completeness assessment performed on publicly available genome and...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2844 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2642 days agolbbe.univ-lyon1.fr - The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...IgBLAST 1.17 is now available with improved identification of productive V gene sequences
By Jit 1952 days agoIgBLAST 1.17 is now available with improved identification of productive V gene sequencesJaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By Neel 205 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies. The performance of the Jaeger...
