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contigs
Here are 31 public repositories matching this topic...
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May 12, 2020 - Perl
noporpoise
commented
Aug 10, 2015
The bubble caller has less power to assemble the reference allele vs sample allele since the reference colour is just a bag of kmers without link information. Reference sequences can provide reasonable link info if we break at repetitive kmers.
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
python
pipeline
docker-image
polymorphic
gap
closing
fasta
scaffolding
assembled-contigs
genome-assembly
paired-end
contigs
heterozygous
mate-pairs
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May 6, 2019 - Perl
Software for prediction of plasmid sequences in metagenomic assemblies
tensorflow
prediction
classification
fasta
plasmid
metagenomes
contigs
metagenome
plasmid-sequences
metagenome-assembly
plasmids
plasflow
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Jun 2, 2020 - Python
Scalable long read self-correction and assembly polishing with multiple sequence alignment
assembly
ngs
consensus
correction
long
self
msa
reads
contigs
long-reads
multiple-sequence-alignment
polishing
self-correction
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Jun 22, 2020 - C++
Simulate metagenomic short reads from one or more populations.
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Jun 7, 2020 - Python
GraphBin: Refined binning of metagenomic contigs using assembly graphs
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Jul 9, 2020 - Python
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
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Jun 30, 2020 - Python
Software to identify plasmid sequence data from metagenome using logistic regression and Minhash
bioinformatics
metagenomics
minhash
classification
logistic-regression
fasta
contigs
metagenome
plasmids
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Nov 19, 2018 - Python
Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files
bioinformatics
genome
contigs
genome-size
extract-sequences
bioinformatics-tool
fasta-files
genomeassembly
renamecontigs
extractcontigs
assemblystatistics
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May 20, 2020 - Shell
A place to store some custom and forked bioinformatic scripts
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May 26, 2020 - Julia
Genome assembly - From theory to practice (and back)
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Apr 1, 2020
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Oct 13, 2019 - Python
Take information about snps on short sequence reads and accurately place the snps in a reference genome
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Jun 26, 2020 - Python
Software to identify known plasmid sequence from metagenomic assembly using Minhash
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Jan 29, 2019 - Go
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
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Jul 8, 2020 - Python
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Dec 11, 2017 - Python
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
visualization
bioinformatics
pipeline
genome
mapping
scaffold
dna
alignment
circos
synteny
act
bioinformatics-analysis
chromosome
contigs
assemblies
smalt
misjoint
rearrengment
inter-chromosomes
minimap2
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May 24, 2020 - C++
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Aug 29, 2018 - Python
Visualize read-to-contig alignment during assembly analysis
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Aug 23, 2018 - Python
Sequencing of unculturable plant pathogens
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Nov 5, 2018 - Shell
Coverage Of COntigs Alignment
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Dec 4, 2018 - C++
A package for fast genomic sequences manipulation or interrogation
python
fast
gzip
genomics
cpp
scaffold
python-script
fasta
fastq
dna-sequences
sequences
contigs
seq-factotum
calculate-stats
print-fasta
fq2fa
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Feb 8, 2018 - C++
Refining Domain Boundaries and Performing Large Scale Parsing
bioinformatics
metagenomics
bioinformatics-pipeline
viruses
protein-domains
contigs
ncbi-virus-discovery-2
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Apr 10, 2020 - Jupyter Notebook
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It would be helpful if FAQ3 in the manual explained interspecies translocation along with inversion and relocation. For instance, in the following:
I'm guessing that positions 1-423 on the reverse strand of k141_1742 translocated to positions 424-1365 on a contig from another species, but I'm j