https://github.com/cellgeni/references
https://github.com/cellgeni/references
Last synced: 4 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/cellgeni/references
- Owner: cellgeni
- License: mit
- Created: 2023-10-09T13:13:18.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-12T01:01:38.000Z (over 1 year ago)
- Last Synced: 2025-09-10T04:57:31.824Z (9 months ago)
- Size: 40 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
- [Fruit Fly](#fruit-fly)
* [BDGP6](#bdgp6)
- [Human](#human)
* [2020A](#2020a)
* [2020A Full](#2020a-full)
* [2020A plus Plasmodium_Falciparum.EPr1.37](#2020a-plus-plasmodium-falciparumepr137)
* [2020A plus GCA_000149715.2_TGGT1_genomic](#2020a-plus-gca-0001497152-tggt1-genomic)
* [Gencode v19 Full](#gencode-v19-full)
* [Gencode v37 Full](#gencode-v37-full)
* [GRCh38-1.2.0](#grch38-120)
* [GRCh38-3.0.0](#grch38-300)
* [GRCh38-3.0.0 plus 3D7](#grch38-300-plus-3d7)
* [GRCh38 15 plus hs38d1 and ensembl 90 transcriptome](#GRCh38-15-plus-hs38d1-and-ensembl-90-transcriptome)
* [hg19-1.2.0](#hg19-120)
* [hg19-3.0.0](#hg19-300)
* [T2T](#t2t)
- [Human with Covid](#human-with-covid)
* [GRCh38 Plus SARSCoV2](#grch38-plus-sarscov2)
- [Human & Mouse](#human---mouse)
* [GRCh38-3.1.0](#grch38-310)
- [Malaria](#malaria)
* [3D7](#3d7)
- [Mouse](#mouse)
* [2020A](#2020a-1)
* [2020A Full](#2020a-full-1)
* [1.2.0](#120)
* [2.1.0](#210)
* [3.0.0](#300)
- [Toxoplasma Gondii](#toxoplasma-gondii)
* [gt1_gca_00149715](#gt1_gca_00149715)
# Fruit Fly
## BDGP6
**STAR version** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/fruit_fly/BDGP6/index
```
**Gene Count:** 23882
**Genome sequence total length:** 137567484
**Chromosome Names:** 2L, 2R, 3L, 3R, 4, mitochondrion_genome, X, Y
**Chromosome Lenght:**
| Chromosome | Length |
|------|-----------|
| 2L | 23513712 |
| 2R | 25286936 |
| 3L | 28110227 |
| 3R | 32079331 |
| 4 | 1348131 |
| mitochondrion_genome | 19524 |
| X | 23542271 |
| Y | 3667352 |
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles /lustre/scratch117/cellgen/cellgeni/TIC-starsolo/tic-1484/fasta/Drosophila_melanogaster.BDGP6.32.dna.primary_assembly.fa --sjdbGTFfile /lustre/scratch117/cellgen/cellgeni/TIC-starsolo/tic-1484/gene_annotation/Drosophila_melanogaster.BDGP6.32.105.chr.gtf --sjdbOverhang 100
```
# Human
## 2020A
**STAR version** 2.7.7a
**Path:**
```
/nfs/cellgeni/STAR/human/2020A/index
```
**Gene Count:** 36601
**Genome sequence total length:** 3099750718
**Chromosome Names:** chr1, chr10, .., chr2, chr20, .., KI270728.1, KI270727.1, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 248956422 |
| chr10 | 133797422 |
| chr11 | 135086622 |
| chr12 | 133275309 |
| chr13 | 114364328 |
| chr14 | 107043718 |
| chr15 | 101991189 |
| chr16 | 90338345 |
| chr17 | 83257441 |
| chr18 | 80373285 |
Please see /nfs/cellgeni/STAR/human/2020A/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STARsolo --genomeFastaFiles GRCh38_v32_modified.fa --sjdbGTFfile GRCh38_v32_filtered.gtf
```
## 2020A Full
**STAR version:** 2.7.7a
**Path:**
```
/nfs/cellgeni/STAR/human/2020A-full/index
```
**Gene Count:** 60668
**Genome sequence total length:** 3099750718
**Chromosome Names:** chr1, chr10, .. , chr2, chr20, .., KI270728.1, KI270727.1, KI270442.1, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 248956422 |
| chr10 | 133797422 |
| chr11 | 135086622 |
| chr12 | 133275309 |
| chr13 | 114364328 |
| chr14 | 107043718 |
| chr15 | 101991189 |
| chr16 | 90338345 |
| chr17 | 83257441 |
| chr18 | 80373285 |
Please see /nfs/cellgeni/STAR/human/2020A-full/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles GRCh38_v32_modified.fa --sjdbGTFfile GRCh38_v32_modified.gtf
```
## 2020A plus Plasmodium_Falciparum.EPr1.37
**STAR version:** 2.7.9a_2021-06-25
**Path:**
```
/nfs/cellgeni/STAR/human/2020A_plus_Pf_3D7/index
```
**Gene Count:** 42294
**Genome sequence total length:** 3123083557
**Chromosome Names:** chr1, ch10, .., chr2, chr20, .., KI270728.1, KI270727.1, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 248956422 |
| chr10 | 133797422 |
| chr11 | 135086622 |
| chr12 | 133275309 |
| chr13 | 114364328 |
| chr14 | 107043718 |
| chr15 | 101991189 |
| chr16 | 90338345 |
| chr17 | 83257441 |
| chr18 | 80373285 |
Please see /nfs/cellgeni/STAR/human/2020A_plus_Pf_3D7/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 16 --genomeDir index --genomeFastaFiles combo.fa --sjdbGTFfile combo.gtf
```
## 2020A plus GCA_000149715.2_TGGT1_genomic
**STAR version:** 2.7.9a_2021-06-25
**Path:**
```
/nfs/cellgeni/STAR/human/2020A_plus_Tg_GT1/index
```
**Gene Count:** 45238
**Genome sequence total length:** 3164812953
**Chromosome Names:** chr1, chr10, chr11, chr12, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 248956422 |
| chr10 | 133797422 |
| chr11 | 135086622 |
| chr12 | 133275309 |
| chr13 | 114364328 |
| chr14 | 107043718 |
| chr15 | 101991189 |
| chr16 | 90338345 |
| chr17 | 83257441 |
| chr18 | 80373285 |
Please see /nfs/cellgeni/STAR/human/2020A_plus_Tg_GT1/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 16 --genomeDir index --genomeFastaFiles combo.fa --sjdbGTFfile combo.gtf
```
## Gencode v19 Full
**STAR version:** 2.7.10a_alpha_220818
**Path:**
```
/nfs/cellgeni/STAR/human/Gencode_v19_full/index
```
**Gene Count:** 63568
**Genome sequence total length:** MISSING INFO HERE
**Chromosome Names:** chr1, chr2, chr3, ...
**Chromosome Lenght:** 3234834689
| Chromosome | Length |
|------------|-----------|
| chr1 | 249250621 |
| chr2 | 243199373 |
| chr3 | 198022430 |
| chr4 | 191154276 |
| chr5 | 180915260 |
| chr6 | 171115067 |
| chr7 | 159138663 |
| chr8 | 146364022 |
| chr9 | 141213431 |
| chr10 | 135534747 |
Please see /nfs/cellgeni/STAR/human/Gencode_v19_full/index/Log.out for more information/Chromosomes
**Build Command:**
```
/opt/STAR-2.7.10a_alpha_220818/source/STAR --runMode genomeGenerate --runThreadN 16 --genomeDir index --genomeFastaFiles GRCh37.p13.genome.fa --sjdbGTFfile gencode.v19.chr_patch_hapl_scaff.annotation.gtf
```
## Gencode v37 Full
**STAR version:** 2.7.10a_alpha_220818
**Path:**
```
/nfs/cellgeni/STAR/human/Gencode_v37_full/index
```
**Gene Count:** 60710
**Genome sequence total length:** 3099750718
**Chromosome Names:** chr,1, chr2, chr3, chr4, ...
**Chromosome Lenght:**
| Chromosome | Length |
|-------|-----------|
| chr1 | 248956422 |
| chr2 | 242193529 |
| chr3 | 198295559 |
| chr4 | 190214555 |
| chr5 | 181538259 |
| chr6 | 170805979 |
| chr7 | 159345973 |
| chr8 | 145138636 |
| chr9 | 138394717 |
| chr10 | 133797422 |
Please see /nfs/cellgeni/STAR/human/Gencode_v37_full/index/Log.out for more information/Chromosomes
**Build Command:**
```
/opt/STAR-2.7.10a_alpha_220818/source/STAR --runMode genomeGenerate --runThreadN 16 --genomeDir index --genomeFastaFiles Gencode_v37_primary.fa --sjdbGTFfile Gencode_v37_primary.gtf
```
## GRCh38-1.2.0
**STAR version:** 2.7.7a
**Path:**
```
/nfs/cellgeni/STAR/human/GRCh38-1.2.0/index
```
**Gene Count:** 33694
**Genome sequence total length:** 3099750718
**Chromosome Names:** 1, 10, 11, 12, 13
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 248956422 |
| 10 | 133797422 |
| 11 | 135086622 |
| 12 | 133275309 |
| 13 | 114364328 |
| 14 | 107043718 |
| 15 | 101991189 |
| 16 | 90338345 |
| 17 | 83257441 |
| 18 | 80373285 |
Please see /nfs/cellgeni/STAR/human/GRCh38-1.2.0/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh38.84.filtered.gtf --sjdbOverhang 90
```
## GRCh38-3.0.0
**STAR version:** 2.7.7a
**Path:**
```
/nfs/cellgeni/STAR/human/GRCh38-3.0.0/index
```
**Gene Count:** 33538
**Genome sequence total length:** 3099750718
**Chromosome Names:** 1, 10, 11, 12, 13, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 248956422 |
| 10 | 133797422 |
| 11 | 135086622 |
| 12 | 133275309 |
| 13 | 114364328 |
| 14 | 107043718 |
| 15 | 101991189 |
| 16 | 90338345 |
| 17 | 83257441 |
| 18 | 80373285 |
Please see /nfs/cellgeni/STAR/human/GRCh38-3.0.0/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh38.93.filtered.gtf --sjdbOverhang 100
```
## GRCh38-3.0.0 plus 3D7
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/human/GRCh38-3.0.0_plus_3D7/index
```
**Gene Count:** 39231
**Genome sequence total length:** 3123083557
**Chromosome Names:** 1, 10, 11, 12
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 248956422 |
| 10 | 133797422 |
| 11 | 135086622 |
| 12 | 133275309 |
| 13 | 114364328 |
| 14 | 107043718 |
| 15 | 101991189 |
| 16 | 90338345 |
| 17 | 83257441 |
| 18 | 80373285 |
Please see /nfs/cellgeni/STAR/human/GRCh38-3.0.0_plus_3D7/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles combo.fa --sjdbGTFfile combo.gtf
```
## GRCh38 15 plus hs38d1 and ensembl 90 transcriptome
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/human/GRCh38_15_plus_hs38d1-and-ensembl_90_transcriptome/star/index
```
**Gene Count:** 60675
**Genome sequence total length:** 3105715063
**Chromosome Names:** chr1, chr2, chr3, chr1_KI270706v1_random, chrUn_GL000216v2, chrUn_GL000218v1, chrEBV, chrUn_KN707606v1_decoy, chrUn_KN707607v1_decoy
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 248956422 |
| chr2 | 242193529 |
| chr3 | 198295559 |
| chr4 | 190214555 |
| chr5 | 181538259 |
| chr6 | 170805979 |
| chr17 | 83257441 |
| chr18 | 80373285 |
| chr19 | 58617616 |
| chr20 | 64444167 |
| chr21 | 46709983 |
| chr22 | 50818468 |
| chrX | 156040895 |
| chrY | 57227415 |
| chrM | 16569 |
| chr1_KI270706v1_random | 175055 |
Please see /nfs/cellgeni/STAR/human/GRCh38_15_plus_hs38d1-and-ensembl_90_transcriptome/star/index/Log.out for more information/Chromosomes
**Build Command:**
```
/software/cellgeni/STAR-2.7.9a/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 16 --genomeDir index --genomeFastaFiles /lustre/scratch125/core/sciops_repository/references/Human/GRCh38_15_plus_hs38d1/all/fasta/Homo_sapiens.GRCh38_15_plus_hs38d1.fa --sjdbGTFfile /nfs/srpipe_references/transcriptomes/Homo_sapiens/ensembl_83_transcriptome/GRCh38_15_plus_hs38d1/gtf/ensembl_83_transcriptome-GRCh38_15_plus_hs38d1.gtf
```
## hg19-1.2.0
**No STAR index built yet**
**Path:**
```
/nfs/cellgeni/STAR/human/hg19-1.2.0
```
## hg19-3.0.0
**No STAR index built yet**
**Path:**
```
/nfs/cellgeni/STAR/human/hg19-3.0.0
```
## T2T
**STAR version:** 2.7.10a_alpha_220818
**Path:**
```
/nfs/cellgeni/STAR/human/T2T/index
```
**Gene Count:** 37274
**Genome sequence total length:** 3117292070
**Chromosome Names:** chr1, chr2, chr3, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 248387328 |
| chr2 | 242696752 |
| chr3 | 201105948 |
| chr4 | 193574945 |
| chr5 | 182045439 |
| chr6 | 172126628 |
| chr7 | 160567428 |
| chrX | 154259566 |
| chr9 | 150617247 |
| chr8 | 146259331 |
Please see /nfs/cellgeni/STAR/human/T2T/index/Log.out for more information/Chromosomes
**Build Command:**
```
/opt/STAR-2.7.10a_alpha_220818/source/STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STARsolo --genomeFastaFiles T2T_with_mito.fa --sjdbGTFfile T2T_v2_filtered.gtf
```
# Human with Covid
## GRCh38 Plus SARSCoV2
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/human_covid/GRCh38_plus_SARSCoV2/index
```
**Gene Count:** 33552
**Genome sequence total length:** 3099780621
**Chromosome Names:** 1, 10, 11, 12, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 248956422 |
| 10 | 133797422 |
| 11 | 135086622 |
| 12 | 133275309 |
| 13 | 114364328 |
| 14 | 107043718 |
| 15 | 101991189 |
| 16 | 90338345 |
| 17 | 83257441 |
| 18 | 80373285 |
Please see /nfs/cellgeni/STAR/human_covid/GRCh38_plus_SARSCoV2/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles human_covid_genome.fa --sjdbGTFfile human_covid_genes.gtf --sjdbOverhang 100
```
# Human & Mouse
## GRCh38-3.1.0
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/human_mouse/GRCh38-3.1.0/index
```
**Gene Count:** 61078
**Genome sequence total length:** 5830622492
**Chromosome Names:** 1, 10, 11, 12, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 248956422 |
| 10 | 133797422 |
| 11 | 135086622 |
| 12 | 133275309 |
| 13 | 114364328 |
| 14 | 107043718 |
| 15 | 101991189 |
| 16 | 90338345 |
| 17 | 83257441 |
| 18 | 80373285 |
Please see /nfs/cellgeni/STAR/human_mouse/GRCh38-3.1.0/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles combined.fa --sjdbGTFfile combined_filtered.gtf --sjdbOverhang 100
```
# Malaria
## 3D7
**STAR version:** 2.7.9a_2021-06-25
**Path:**
```
/nfs/cellgeni/STAR/malaria/3D7/index
```
**Gene Count:** 5693
**Genome sequence total length:** 23332839
**Chromosome Names:** Pf3D7_01_v3, Pf3D7_02_v3, Pf3D7_03_v3, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| Pf3D7_01_v3 | 640851 |
| Pf3D7_02_v3 | 947102 |
| Pf3D7_03_v3 | 1067971 |
| Pf3D7_04_v3 | 1200490 |
| Pf3D7_05_v3 | 1343557 |
| Pf3D7_06_v3 | 1418242 |
| Pf3D7_07_v3 | 1445207 |
| Pf3D7_08_v3 | 1472805 |
| Pf3D7_09_v3 | 1541735 |
| Pf3D7_10_v3 | 1687656 |
Please see /nfs/cellgeni/STAR/malaria/3D7/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 16 --genomeDir index --genomeFastaFiles ensembl_37_genome-3D7_Jan16v3.fa --genomeSAindexNbases 11 --sjdbGTFfile Plasmodium_falciparum.EPr1.37.gtf
```
# Mouse
## 2020A
**STAR version:** 2.7.7a
**Path:**
```
/nfs/cellgeni/STAR/mouse/2020A/index
```
**Gene Count:** 32285
**Genome sequence total length:** 2730871774
**Chromosome Names:** chr1, chr10, chr11, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 195471971 |
| chr10 | 130694993 |
| chr11 | 122082543 |
| chr12 | 120129022 |
| chr13 | 120421639 |
| chr14 | 124902244 |
| chr15 | 104043685 |
| chr16 | 98207768 |
| chr17 | 94987271 |
| chr18 | 90702639 |
Please see /nfs/cellgeni/STAR/mouse/2020A/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles mm10_vM23_modified.fa --sjdbGTFfile mm10_vM23_filtered.gtf --sjdbOverhang 100
```
## 2020A Full
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/mouse/2020A-full/index
```
**Gene Count:** 55421
**Genome sequence total length:** 2730871774
**Chromosome Names:** chr1, chr10, chr11, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| chr1 | 195471971 |
| chr10 | 130694993 |
| chr11 | 122082543 |
| chr12 | 120129022 |
| chr13 | 120421639 |
| chr14 | 124902244 |
| chr15 | 104043685 |
| chr16 | 98207768 |
| chr17 | 94987271 |
| chr18 | 90702639 |
Please see /nfs/cellgeni/STAR/mouse/2020A-full/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir index --genomeFastaFiles mm10_vM23_modified.fa --sjdbGTFfile mm10_vM23_modified.gtf
```
## 1.2.0
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/mouse/1.2.0/index
```
**Gene Count:** 27998
**Genome sequence total length:** 2730871774
**Chromosome Names:** 1, 10, 11, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 195471971 |
| 10 | 130694993 |
| 11 | 122082543 |
| 12 | 120129022 |
| 13 | 120421639 |
| 14 | 124902244 |
| 15 | 104043685 |
| 16 | 98207768 |
| 17 | 94987271 |
| 18 | 90702639 |
Please see /nfs/cellgeni/STAR/mouse/1.2.0/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.84.filtered.gtf --sjdbOverhang 90
```
## 2.1.0
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/mouse/2.1.0/index
```
**Gene Count:** 28692
**Genome sequence total length:** 2730871774
**Chromosome Names:** 1, 10, 11, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 195471971 |
| 10 | 130694993 |
| 11 | 122082543 |
| 12 | 120129022 |
| 13 | 120421639 |
| 14 | 124902244 |
| 15 | 104043685 |
| 16 | 98207768 |
| 17 | 94987271 |
| 18 | 90702639 |
Please see /nfs/cellgeni/STAR/mouse/2.1.0/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.84.filtered.gtf --sjdbOverhang 90
```
## 3.0.0
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/mouse/3.0.0/index
```
**Gene Count:** 31053
**Genome sequence total length:** 2730871774
**Chromosome Names:** 1, 10, 11, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| 1 | 195471971 |
| 10 | 130694993 |
| 11 | 122082543 |
| 12 | 120129022 |
| 13 | 120421639 |
| 14 | 124902244 |
| 15 | 104043685 |
| 16 | 98207768 |
| 17 | 94987271 |
| 18 | 90702639 |
Please see /nfs/cellgeni/STAR/mouse/3.0.0/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.93.filtered.gtf --sjdbOverhang 90
```
# Toxoplasma Gondii
## gt1_gca_00149715
**STAR version:** 2.7.9a
**Path:**
```
/nfs/cellgeni/STAR/Toxoplasma_gondii/gt1_gca_00149715/index
```
**Gene Count:** 8637
**Genome sequence total length:** 65062235
**Chromosome Names:** KE387274.1, KE387275.1, KE387276.1, ...
**Chromosome Lenght:**
| Chromosome | Length |
|------------|-----------|
| KE387274.1 | 6945667 |
| KE387275.1 | 384772 |
| KE387276.1 | 6795584 |
| KE387277.1 | 4721207 |
| KE387278.1 | 4666718 |
| KE387279.1 | 4652972 |
| KE387280.1 | 4225262 |
| KE387281.1 | 859182 |
| KE387282.1 | 43610 |
| KE387283.1 | 2730344 |
Please see /nfs/cellgeni/STAR/Toxoplasma_gondii/gt1_gca_00149715/index/Log.out for more information/Chromosomes
**Build Command:**
```
STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR --genomeFastaFiles GCA_000149715.2_TGGT1_genomic.fna --genomeSAindexNbases 11 --sjdbGTFfile GCA_000149715.2_TGGT1_genomic.gtf --sjdbOverhang 100
```