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awesome-linked-reads
Collection of tools and resources for linked-reads
https://github.com/pontushojer/awesome-linked-reads
- Aldy - commit/0xTCG/aldy?label=%20)
- Ambigram - fusion-bridge genome rearrangements that supports linked-reads|
- Aquila - reads|
- Aquila_stLFR - resolved assembly and variant detection for stLFR, hybrid assembly for linked-reads|
- AquilaDeepFilter - wide false positive large deletions|
- AquilaSV - based phased diploid assemblies for 10X and stLFR linked-reads|
- ARBitR - commit/markhilt/ARBitR?label=%20)
- Ariadne - based program for barcoded read deconvolution|
- arcs - commit/bcgsc/arcs?label=%20)
- Athena - commit/abishara/athena_meta?label=%20)
- BarCrawler - commit/J35P312/BarCrawler?label=%20)
- bcctools - read sequencing data|
- bcmap - commit/kehrlab/bcmap?label=%20)
- BLR - to-end Snakemake workflow for whole genome haplotyping and structural variant calling from FASTQs from multiple linked-read technologies.|
- bxtools - commit/walaj/bxtools?label=%20)
- cloudSPAdes - commit/ablab/spades/cloudspades-ismb?label=%20)
- ChromeQC - commit/bcgsc/chromeqc?label=%20)
- Cue - commit/PopicLab/cue?label=%20)
- DrLink - commit/schneebergerlab/DrLink?label=%20)
- EMerAld (EMA) - aware alignment of linked reads. Also does preprocessing of 10x Genomics data.|
- Gemtools - read sequencing (10X Genomics) data|
- grocsvs - wide reconstruction of complex structural variants|
- HapCUT2 - commit/vibansal/HapCUT2?label=%20)
- HapTree-X - generation sequencing data|
- HARPY - commit/pdimens/harpy?label=%20)
- HAST - Resolved Assembly for Synthetic Long Reads Using A Trio-Binning Strategy|
- Lancet - read data|
- Lariat - Read Alignment Tool|
- LEVIATHAN - reads based structural variant caller with barcode indexing|
- Link_STR - read data|
- LinkedSV - read sequencing data|
- Linker - commit/rwtourdot/linker?label=%20)
- LongRanger - commit/10XGenomics/longranger?label=%20)
- LRez - reads|
- LRTK-SIM - commit/zhanglu295/LRTK-SIM?label=%20)
- LRSIM - commit/aquaskyline/LRSIM?label=%20)
- MetaTrass - commit/BGI-Qingdao/MetaTrass?label=%20)
- Minerva - commit/dcdanko/minerva_barcode_deconvolution?label=%20)
- mLinker - commit/chengzhongzhangDFCI/GenomeBiology-mLinker?label=%20)
- MTG-Link - filling tool for draft genome assemblies, dedicated to linked read data|
- NAIBR - commit/raphael-group/NAIBR?label=%20)<br />
- Novel-X - commit/1dayac/Novel-X?label=%20)
- NPGREAT - Reads datasets for the assembly of the human subtelomere regions.|
- Pangaea - reads with high-barcode specificity|
- proc10xG - commit/ucdavis-bioinformatics/proc10xG?label=%20)
- Pseudoseq - commit/bioinfologics/Pseudoseq.jl?label=%20)
- Pyslr - commit/bcgsc/physlr?label=%20)
- QuickDeconvolution - reads experiments without a reference genome |
- Samovar - based filters|
- samplot - commit/ryanlayer/samplot?label=%20)
- Scaff10x (v5) - commit/wtsi-hpag/Scaff10X?label=%20)
- SpecHLA - commit/deepomicslab/SpecHLA?label=%20)
- SpLitteR
- stLFRdenovo - commit/BGI-biotools/stLFRdenovo?label=%20)
- stLFRsv - barcode reads|
- SuperNova - Read Diploid De Novo Assembler|
- SVenX - commit/vborjesson/SVenX?label=%20)
- tenx_utils - commit/friend1ws/tenx_utils?label=%20)
- Tigmint - commit/bcgsc/tigmint?label=%20)
- TitanCNA_10x - commit/GavinHaLab/TitanCNA_10X_snakemake?label=%20)
- Topsorter - commit/hanfang/Topsorter?label=%20)
- VISOR - commit/davidebolo1993/VISOR?label=%20)
- Valor - reads|
- WhatsHap - based phasing of genomic variants, also called haplotype assembly. Implements several tools which work with linked reads|
- Wrath - commit/annaorteu/wrath?label=%20)
- xTea - commit/parklab/xTea?label=%20)
- ZoomX
- GemCode (v1) - containing gel-beads to create GEMs ((Gel Bead-In EMulsions). The fragments are amplified and barcoded using a combination of free random hexamers and barcode-linked random hexamers from the gel beads. Following this barcoded fragments are recovered and fragments before ligation of 3' sequencing adaptor. Libraries are sequenced using Illumina Sequencing. The commercial version of the technology is [currently discontinued](https://www.10xgenomics.com/products/linked-reads).
- Chen et al. 2020
- Wang et al. 2019 - tech.com/products/reagents_info/18/). The technology uses tagmentation to individually cut-and-hold long DNA fragments in solution. The tagmentase-DNA complex is then hybridized and individual wrapped around barcoded beads through the adaptor introduced by the tagmentation. The barcode is then ligated to each subfragment before recovery and final library prepration. Sequencing is preformed on the DNBSEQ platfroms.
- Redin el al. 2019 - covered beads to cut, tag and wrap the fragment around the beads. The DNA-wrapped beads are then used in emmulsion PCR along with barcoded oligo. Within each emmulsion droplet the barcode and tagged fragments are amplified independently and then linked using overlap-extension. Barcode-linked fragments are recovered and indexed for Illumina sequencing.
- Amini et al. 2014 - up CPTv2-seq from [Zhang et al. 2017](https://doi.org/10.1038/nbt.3897). These technologies were developed by Illumina but are not commercially available.
- Meier et al. 2021
- Awesome-10x-genomics
Programming Languages
Keywords
bioinformatics
11
linked-reads
10
10xgenomics
6
genome
3
sequencing
3
genomics
3
barcodes
3
genome-assembly
3
illumina
2
graph
2
genome-scaffolding
2
bioinformatics-tool
2
pipeline
2
10x-genomics
2
pacbio-data
2
nanopore
2
haplotype
2
assembly
2
local-assembly
2
mobile-element-insertion
1
pacbio
1
transposable-elements
1
adme
1
allele
1
cyp2d6
1
genotype
1
pgrnseq
1
cancer
1
assembler
1
c-plus-plus
1
allelic-imbalance
1
genotype-frequency
1
topological-sort
1
hla-sequence
1
hla-typing
1
misassembly-correction
1
human-leukocyte-antigens
1
immunity
1
loh
1
loss-of-heterozygosity
1
structural-variations
1
reads-binning
1
phase
1
index
1
linked
1
reads
1
stlfr
1
tell-seq
1
computational-biology
1
human-genomes
1