transcriptome-assembly
There are 31 repositories under transcriptome-assembly topic.
ablab/spades
SPAdes Genome Assembler
bcgsc/transabyss
de novo assembly of RNA-seq data using ABySS
cfarkas/annotate_my_genomes
A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes
ablab/rnaquast
Quality assessment of de novo transcriptome assemblies from RNA-Seq data
macmanes-lab/Oyster_River_Protocol
Official Repository of the Oyster River Protocol for Transcriptome Assembly
bcgsc/ChopStitch
Finding putative exons and constructing splicegraphs using Trans-ABySS contigs
bethsheets/palumbi_scripts
Most up-to-date scripts used in the Palumbi lab
dn070017/QuantEval
QuantEval is an analysis pipeline which evaluate the reliability of quantification tools.
LiLabZhaohua/PacBioWorkflow
A collection of scripts for our PacBio paper
jlanga/smsk_khmer_trinity
Transcriptome assembly via digital normalization with khmer and Trinity
jungsoh/transcriptomics-course
Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining
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
biocorecrg/transcriptome_assembly
Biocore's de novo transcriptome assembly workflow based on Nextflow
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
Shao-Group/aletsch
Assembler for multiple RNA-seq samples
sunyumail93/PacBioWorkflow
A collection of scripts for our PacBio paper
TF-Chan-Lab/LAFITE
tool for long read transcriptome assembly
jlanga/khmer_trinity_snakemake
A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity
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.
PapenfussLab/assemble_var
A pipeline for the assembly of VAR genes from transcriptome data
shinichinamba/MuSTA
MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing
zyxue/vr2c
Visualize read-to-contig alignment during assembly analysis
jazminvaleriano/RNAseq-differential-expression
Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.
holsapple/Trinity-analysis
an investigation into the efficiency of Trinity transcriptome assemblies
juliawiggeshoff/rna-seq-2x-de-novo-assembly
Snakemake workflow to de novo assemble transcriptomes with two software, Trinity and Shannon. Imported from my GitLab.
roblehmann/marineHeatwave
Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"
tfording/asp_inornata
a_inornata research project
codecreatede/trinity-analyzer
from trinity assembly to deep learning
Indronil-Prince/Transcriptome-Assembly
Bioinformatics Programming - Transcriptome Assembly
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.
zyxue/kleat
Cleavage site prediction via de novo assembly