Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: transcriptome-assembly
Shao-Group/aletsch
Assembler for multiple RNA-seq samples
Language: C++ - Size: 9.82 MB - Last synced: about 7 hours ago - Pushed: about 9 hours ago - Stars: 0 - Forks: 1
ablab/spades
SPAdes Genome Assembler
Language: C++ - Size: 97 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 689 - Forks: 130
gauravcodepro/transdecoder-visualization
a regular expression based trinity assembly transdecoder predictions encoder which will parse and will prepare the transcript annotations for visualization with any genome visualization kit such as pygenomeviz, mauve and others, it prepares the coordinates as tuples
Language: Python - Size: 18.6 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
gauravcodepro/tair-gff-ids
A set of functions which will provide easy access and cleaned gff from tair and uses a dataframe and datascience approach to get the systematic tair ids and their coordinates from the tair 10 gff version. It can be applied to any version of the tair for getting the systematic retrival of the tair ids.
Language: Python - Size: 4.69 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
gauravcodepro/trinity-blast-machine-learning
a scalable and faster implementation for the genome and the transcriptome annotations for large scale sequencing datasets.
Language: Python - Size: 48.8 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
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: 2 months ago - Pushed: 2 months ago - Stars: 22 - Forks: 4
ablab/rnaquast
Quality assessment of de novo transcriptome assemblies from RNA-Seq data
Language: Python - Size: 6.04 MB - Last synced: 20 days ago - Pushed: 10 months ago - Stars: 17 - Forks: 6
bcgsc/transabyss
de novo assembly of RNA-seq data using ABySS
Language: Python - Size: 724 KB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 33 - Forks: 13
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: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
PapenfussLab/assemble_var
A pipeline for the assembly of VAR genes from transcriptome data
Language: HTML - Size: 90.1 MB - Last synced: 6 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 2
jlanga/khmer_trinity_snakemake 📦
A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity
Language: Python - Size: 42.8 MB - Last synced: 8 months ago - Pushed: about 7 years ago - Stars: 2 - Forks: 4
holsapple/Trinity-analysis
an investigation into the efficiency of Trinity transcriptome assemblies
Language: Python - Size: 4.88 KB - Last synced: 8 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0
bethsheets/palumbi_scripts
Most up-to-date scripts used in the Palumbi lab
Language: Python - Size: 159 KB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 7 - Forks: 4
biocorecrg/transcriptome_assembly
Biocore's de novo transcriptome assembly workflow based on Nextflow
Language: Nextflow - Size: 2.42 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 2
TF-Chan-Lab/LAFITE
tool for long read transcriptome assembly
Language: Jupyter Notebook - Size: 46.5 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 3 - Forks: 1
roblehmann/marineHeatwave
Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"
Size: 563 KB - Last synced: 11 months ago - Pushed: 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: about 1 year ago - Pushed: about 1 year 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: 5 months ago - Pushed: about 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: 5 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0
macmanes-lab/Oyster_River_Protocol
Official Repository of the Oyster River Protocol for Transcriptome Assembly
Language: TeX - Size: 58 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 16 - Forks: 13
shinichinamba/MuSTA
MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing
Language: Shell - Size: 1.54 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2
sunyumail93/PacBioWorkflow
A collection of scripts for our PacBio paper
Language: C++ - Size: 32.5 MB - Last synced: over 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
LiLabZhaohua/PacBioWorkflow
A collection of scripts for our PacBio paper
Language: C++ - Size: 34.9 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 4 - Forks: 1
dn070017/QuantEval
QuantEval is an analysis pipeline which evaluate the reliability of quantification tools.
Language: Python - Size: 4.92 MB - Last synced: 8 months ago - Pushed: almost 4 years ago - Stars: 8 - Forks: 1
zyxue/vr2c
Visualize read-to-contig alignment during assembly analysis
Language: Python - Size: 66.4 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0
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: 12 months ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 0
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: over 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
bcgsc/ChopStitch
Finding putative exons and constructing splicegraphs using Trans-ABySS contigs
Language: C++ - Size: 349 KB - Last synced: 8 months ago - Pushed: over 5 years ago - Stars: 12 - Forks: 1
jlanga/smsk_khmer_trinity
Transcriptome assembly via digital normalization with khmer and Trinity
Language: Python - Size: 474 KB - Last synced: 8 months ago - Pushed: about 5 years ago - Stars: 4 - Forks: 2
zyxue/kleat
Cleavage site prediction via de novo assembly
Language: Python - Size: 14 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0