Topic: "transcriptome-assembly"
ablab/spades
SPAdes Genome Assembler
Language: C++ - Size: 97.6 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 820 - Forks: 149
bcgsc/transabyss
de novo assembly of RNA-seq data using ABySS
Language: Python - Size: 724 KB - Last synced at: 24 days ago - Pushed at: almost 2 years ago - Stars: 34 - Forks: 14
cfarkas/annotate_my_genomes
A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes
Language: Nextflow - Size: 29.4 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 22 - Forks: 4
ablab/rnaquast
Quality assessment of de novo transcriptome assemblies from RNA-Seq data
Language: Python - Size: 6.07 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 17 - Forks: 6
macmanes-lab/Oyster_River_Protocol
Official Repository of the Oyster River Protocol for Transcriptome Assembly
Language: TeX - Size: 58 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 16 - Forks: 13
ishinder/EASTR
Emending Alignment of Spliced Transcript Reads
Language: Python - Size: 334 KB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 11 - Forks: 1
bcgsc/ChopStitch
Finding putative exons and constructing splicegraphs using Trans-ABySS contigs
Language: C++ - Size: 349 KB - Last synced at: 24 days ago - Pushed at: over 6 years ago - Stars: 11 - Forks: 1
dn070017/QuantEval
QuantEval is an analysis pipeline which evaluate the reliability of quantification tools.
Language: Python - Size: 4.92 MB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 1
bethsheets/palumbi_scripts
Most up-to-date scripts used in the Palumbi lab
Language: Python - Size: 159 KB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 7 - Forks: 4
Shao-Group/aletsch
Assembler for multiple RNA-seq samples
Language: C++ - Size: 9.99 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 1
LiLabZhaohua/PacBioWorkflow
A collection of scripts for our PacBio paper
Language: C++ - Size: 34.9 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 1
jlanga/smsk_khmer_trinity
Transcriptome assembly via digital normalization with khmer and Trinity
Language: Python - Size: 474 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 2
biocorecrg/transcriptome_assembly
Biocore's de novo transcriptome assembly workflow based on Nextflow
Language: Nextflow - Size: 2.42 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 2
TF-Chan-Lab/LAFITE
tool for long read transcriptome assembly
Language: Jupyter Notebook - Size: 46.5 MB - Last synced at: 17 days ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 1
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
Language: Shell - Size: 32.8 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 0
PapenfussLab/assemble_var
A pipeline for the assembly of VAR genes from transcriptome data
Language: HTML - Size: 90.1 MB - Last synced at: 2 days ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 3
shinichinamba/MuSTA
MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing
Language: Shell - Size: 1.54 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 2
zyxue/vr2c
Visualize read-to-contig alignment during assembly analysis
Language: Python - Size: 66.4 KB - Last synced at: 2 months ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0
jlanga/khmer_trinity_snakemake 📦
A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity
Language: Python - Size: 42.8 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 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
Language: HTML - Size: 20.3 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
sunyumail93/PacBioWorkflow
A collection of scripts for our PacBio paper
Language: C++ - Size: 32.5 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
NIGMS/Transcriptome-Assembly-Refinement-and-Applications
In this module, you will learn how to use a Nextflow pipeline to assemble and annotate a novel transcriptome using RNA-seq data
Language: Jupyter Notebook - Size: 6.13 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 4
IBCHgenomic/trinity-analyzer
from trinity assembly to deep learning
Language: Python - Size: 1.95 KB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
jazminvaleriano/RNAseq-differential-expression
Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.
Language: Shell - Size: 272 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
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.
Language: Python - Size: 136 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
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.
Language: R - Size: 4.88 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 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.
Language: Python - Size: 23.4 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
roblehmann/marineHeatwave
Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"
Size: 563 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
zyxue/kleat
Cleavage site prediction via de novo assembly
Language: Python - Size: 14 MB - Last synced at: about 2 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
holsapple/Trinity-analysis
an investigation into the efficiency of Trinity transcriptome assemblies
Language: Python - Size: 4.88 KB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0
