transcriptome-assembly

There are 0 repository under transcriptome-assembly topic.

• ablab / spades

  SPAdes Genome Assembler

  genome-assemblysequence-assemblersequencingtranscriptome-assemblyilluminametagenome-assemblynext-generation-sequencing
  Language:C++ 725

• bcgsc / transabyss

  de novo assembly of RNA-seq data using ABySS

  transcriptometranscriptome-assemblyrna-seqbioinformatics
  Language:Python 33

• cfarkas / annotate_my_genomes

  A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes

  transcriptome-assemblytranscriptomegenome-annotationrna-seqstringtiebraker2
  Language:Nextflow 27

• ablab / rnaquast

  Quality assessment of de novo transcriptome assemblies from RNA-Seq data

  quality-evaluationtranscriptome-assembly
  Language:Python 17

• macmanes-lab / Oyster_River_Protocol

  Official Repository of the Oyster River Protocol for Transcriptome Assembly

  transcriptome-assemblyoyster-river-protocolassemblygenomicsrnaseq
  Language:TeX 16

• bcgsc / ChopStitch

  Finding putative exons and constructing splicegraphs using Trans-ABySS contigs

  transcriptome-assemblyputative-exonssplicesplice-graphsexonbloom-filter
  Language:C++ 12

• bethsheets / palumbi_scripts

  Most up-to-date scripts used in the Palumbi lab

  transcriptome-assemblysnpsblast
  Language:Python 8

• dn070017 / QuantEval

  QuantEval is an analysis pipeline which evaluate the reliability of quantification tools.

  quantification-evaluation-methodstranscriptome-assemblyconnected-components
  Language:Python 8

• LiLabZhaohua / PacBioWorkflow

  A collection of scripts for our PacBio paper

  pacbio-iso-seqtranscriptome-assembly
  Language:C++ 5

• jlanga / smsk_khmer_trinity

  Transcriptome assembly via digital normalization with khmer and Trinity

  transcriptome-assemblyngstrinitykhmerdigital-normalizationassemblertransratesnakemake
  Language:Python 4

• jungsoh / transcriptomics-course

  Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining

  transcriptomicstranscriptome-assemblytranscriptome-annotationde-novo-assemblydifferential-expression-analysisfunctional-annotationannotation-data
  Language:HTML 4

• katarinastuart / Sv3_StarlingGenome

  Scripts and notes related to the manuscript: Stuart KC & Edwards RJ et al. 2022. Transcript- and annotation-guided genome assembly of the European starling. Molecular Ecology Resources, doi.org/10.1101/2021.04.07.438753. † joint first author

  genome-annotationgenome-assemblyiso-seqtranscriptome-assemblyavian-genomegenome-assessment
  Language:Shell 4

• biocorecrg / transcriptome_assembly

  Biocore's de novo transcriptome assembly workflow based on Nextflow

  denovo-assemblytranscriptome-assembly
  Language:Nextflow 3

• mppl1 / RNAseq_preprocessing

  These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

  rnaseq-pipelinehisat2stringtietranscriptome-assemblydifferential-gene-expression
  Language:Shell 3

• sunyumail93 / PacBioWorkflow

  A collection of scripts for our PacBio paper

  pacbio-iso-seqtranscriptome-assembly
  Language:C++ 3

• TF-Chan-Lab / LAFITE

  tool for long read transcriptome assembly

  nanoporedirect-rna-sequencinglong-readtranscriptome-assembly
  Language:Jupyter Notebook 3

• jlanga / khmer_trinity_snakemake

  A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity

  trinitykhmertranscriptome-assemblypipelinesnakemake
  Language:Python 2

• juliawiggeshoff / AugusMake

  The AugusMake pipeline is a Snakemake-based workflow for generating gene annotations using the Augustus software. AugusMake can perform gene predictions using any combination of the three methods: ab initio, with extrinsic hints, or by training a new species.

  augustusgene-predictionreproducibilityrna-seqsnakemaketranscriptome-assemblyworkflow
  Language:Python 2

• Shao-Group / aletsch

  Assembler for multiple RNA-seq samples

  rna-seqtranscriptome-assemblymeta-assemblysingle-cell
  Language:C++ 2

• shinichinamba / MuSTA

  MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing

  long-readtranscriptometranscriptome-assemblyisoseq-3multi-samples
  Language:Shell 2

• zyxue / vr2c

  Visualize read-to-contig alignment during assembly analysis

  genome-assemblytranscriptome-assemblycontig-coveragecontigsalignmentread-to-contig-alignment
  Language:Python 2

• jazminvaleriano / RNAseq-differential-expression

  Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.

  bedtoolsdifferential-expressionkallistorna-seqsleuthtranscriptome-assembly
  Language:Shell 1

• PapenfussLab / assemble_var

  A pipeline for the assembly of VAR genes from transcriptome data

  vartranscriptome-assembly
  Language:HTML 1

• holsapple / Trinity-analysis

  an investigation into the efficiency of Trinity transcriptome assemblies

  transcriptome-assemblygenome-assemblybioinformaticsbioinformatics-pipeline
  Language:Python 0

• juliawiggeshoff / rna-seq-2x-de-novo-assembly

  Snakemake workflow to de novo assemble transcriptomes with two software, Trinity and Shannon. Imported from my GitLab.

  rna-seqshannonsnakemaketranscriptome-assemblytrinityworkflow
  Language:Python 0
• marineHeatwave

  roblehmann / marineHeatwave

  Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"

  bioinformaticsdifferential-expressionorthologstranscriptome-assembly
  0

• tfording / asp_inornata

  a_inornata research project

  benchmarkinggenome-annotationtranscriptome-assembly
  Language:HTML 0

• gauravcodepro / tair-gff-ids

  ease of access gff files from tair for reading tair ids.

  genomegenome-analysisgenome-annotationgenome-assemblygenome-sequencingtairtair3transcriptome-annotationtranscriptome-assembly
  Language:Python

• gauravcodepro / transdecoder-visualization

  transdecoder predictions analyzer for pygenomeviz, mauve.

  genepredictiongenome-annotationtranscriptome-analysistranscriptome-annotationtranscriptome-assemblytranscriptome-widetrinity
  Language:Python

• gauravcodepro / trinity-blast-machine-learning

  from trinity assembly to deep learning.

  bacterial-genome-analysisbacterial-genomesgenome-annotationgenome-assemblyplantgenomesplantgenomicstranscriptome-annotationtranscriptome-assemblytranscriptome-profiling-datatranscriptome-widetranscriptomicstrinity
  Language:Python

• Indronil-Prince / Transcriptome-Assembly

  Bioinformatics Programming - Transcriptome Assembly

  bioinformaticsrhisat2starigvsplicingtranscriptome-assembly
  Language:Jupyter Notebook

• sivkri / rna-Seq-ScaledLengthTPM

  To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.

  tpmtranscriptome-assemblygene-expressiongenomicsgenomics-analysisrna-seqrna-seq-analysisrnaseqtranscripts-per-million
  Language:R

• zyxue / kleat

  Cleavage site prediction via de novo assembly

  de-novo-assemblyalternative-polyadenylationrna-seqtranscriptome-assemblycleavage-sites
  Language:Python