47 skills found · Page 2 of 2
hacchy / MetaVelvetAn extension of Velvet assembler to de novo metagenome assembly from short sequence reads
NancyZxll / Temperate Phage Active Prophage Detectiondetect temperate phage (active prophage) in assembled bacterial genome sequences
b-brankovics / GrabbGRAbB (Genome Region Assembly by Baiting) is a program designed to assemble selected regions of the genome or transcriptome using reference sequences and NGS data.
cumbof / MetaSBTA scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees
msGenDev / Bioinformatics AlgorithmsPython code covering some of the algorithms underlying the following fundamental topics in bioinformatics: assembling genomes, comparing DNA and protein sequences, finding regulatory motifs, analyzing genome rearrangements, identifying proteins, and many other topics.
YoukaiFromAccounting / Skandiverskandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequences using average nucleotide identity (ANI)
krixik-ai / Python ClientEasily assemble and consume modular pipelines of sequenced AI models.
ChandraPedamallu / PathSeqWe present a customizable computational tool, PathSeq2.0, to enable the discovery and identification of microbial sequences in metagenomic samples. This is a flexible, user-adaptable, pipeline that is easily assembled using a configuration file tailored towards particular sequencing experiment parameters such as type of sequencing library, sample of origin, sequencing technology, host species and library read length. PathSeq2.0 also provides auxiliary tools that facilitate the identification of viral integration sites within the host genome and quantification of microbial abundance in the sample set.
avantonder / AssembleBAC ONTavantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.
BirolLab / PASSProteome Assembler with Short peptide Sequence
0x002A / MuCHSALSAMulti-Core Hybrid Short- And Long-read Sequence Assembler
wum5 / JaltGenomeRaw scripts for de novo assembling a Jaltomata genome. Publication: Wu, M., Kostyun, J. and Moyle, L., 2018. Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae. Genome Biology and Evolution, evy274.
BirolLab / GoldpolishGoldPolish (aka GoldRush-Edit) is a long read sequence polisher used in the GoldRush assembler
karla-vasco / Metagenomic ResistomeThis repository contains all the scripts used for metagenomic processing and resistome. First, metagenome sequences from cattle feces were analyzed with AmrPlusPlus for sequence processing and ARG annotations with the MEGARES 2.0 database. Then, host-removed metagenomes were used for DNA assembly and further annotations with DeepARG, CARD, and HMD-ARG which are protein databases to identify antimicrobial determinants. Finally, ARG-host identification was carried out by identifying taxa associated with ARG-carrying contigs and co-occurrence networks between bacterial taxa and ARGs. Statistical analyses were used to identify assembler performance and resistome composition.
adadiehl / GPatchAssemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
CSCLabTW / CloudBrushA De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework
iiiir / GRCH38 Gatk Bundleliftover version of the gatk resource bundle for the new assembling GRCH38 (primary assembling, no alt contigs or decoy sequences).
mahulchak / Mito FinderAssembling mitochondrial genomes from long molecule sequences
0Petya / Debruijn AssemblerAn online De Bruijn graph sequence assembler
kelkar / Discover PseudogenesDiscover pseudogenes in a newly assembled genome, using reference gene/protein sequences.
