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snp-pileup
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public |
Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets
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2024-09-17 |
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r-facets
|
public |
Cellular Fraction and Copy Numbers from Tumor Sequencing
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2024-09-17 |
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cnv_facets
|
public |
Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data
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2024-09-17 |
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alfred
|
public |
BAM alignment statistics, feature counting and feature annotation
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2024-09-16 |
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bx-python
|
public |
Tools for manipulating biological data, particularly multiple sequence alignments
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2024-09-16 |
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pronto
|
public |
Python frontend to ontologies
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2024-09-15 |
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mummer
|
public |
MUMmer is a system for rapidly aligning entire genomes
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2024-09-13 |
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bioconvert
|
public |
Convert between bioinformatics formats
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2024-09-13 |
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bcftools
|
public |
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
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2024-09-12 |
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samtools
|
public |
Tools for dealing with SAM, BAM and CRAM files
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2024-09-12 |
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htslib
|
public |
C library for high-throughput sequencing data formats.
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2024-09-12 |
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abyss
|
public |
Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler
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2024-09-12 |
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gdc-client
|
public |
GDC Data Transfer Tool
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2024-09-11 |
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mcl
|
public |
MCL - a cluster algorithm for graphs
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2024-09-11 |
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synapseclient
|
public |
Python client for Synapse
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2024-09-10 |
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moods
|
public |
MOODS: Motif Occurrence Detection Suite
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2024-09-10 |
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toulligqc
|
public |
A post sequencing QC tool for Oxford Nanopore sequencers.
|
2024-09-10 |
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shortstack
|
public |
ShortStack: Comprehensive annotation and quantification of small RNA genes
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2024-09-10 |
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sra-tools
|
public |
The SRA Toolkit and SDK from NCBI.
|
2024-09-10 |
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freebayes
|
public |
Bayesian haplotype-based polymorphism discovery and genotyping
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2024-09-10 |
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ncbi-vdb
|
public |
SRA tools database engine
|
2024-09-10 |
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r-stitch
|
public |
STITCH - Sequencing To Imputation Through Constructing Haplotypes.
|
2024-09-10 |
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perl-mce
|
public |
Many-Core Engine for Perl providing parallel processing capabilities
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2024-09-10 |
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perl-mce-shared
|
public |
MCE extension for sharing data supporting threads and processes
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2024-09-10 |
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graphmap
|
public |
A highly sensitive and accurate mapper for long, error-prone reads
|
2024-09-09 |
|
truvari
|
public |
Structural variant comparison tool for VCFs
|
2024-09-09 |
|
eigensoft
|
public |
The EIGENSOFT package implements methods for analzing population structure and performing stratification correction
|
2024-09-09 |
|
scnic
|
public |
SCNIC: Sparse Cooccurence Network Investigation for Compositional data
|
2024-09-06 |
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egglib
|
public |
Evolutionary Genetics and Genomics Library. EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, and coalescent simulations. EggLib is a flexible Python module with a performant underlying C++ library and allows fast and intuitive development of Python programs and scripts.
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2024-09-06 |
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python-edlib
|
public |
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
|
2024-09-05 |
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clipandmerge
|
public |
Clip&Merge is a tool to clip off adapters from sequencing reads and merge overlapping paired end reads together.
|
2024-09-05 |
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dedup
|
public |
DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
|
2024-09-05 |
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last
|
public |
LAST finds & aligns related regions of sequences.
|
2024-09-03 |
|
spaln
|
public |
Map and align a set of cDNA/EST or protein sequences onto a genome
|
2024-09-03 |
|
perl-graph
|
public |
a Perl extension for keeping data partially sorted
|
2024-09-02 |
|
tigmint
|
public |
Correct misassemblies using linked or long reads
|
2024-09-01 |
|
python-bioext
|
public |
A few handy bioinformatics tools not already in BioPython
|
2024-08-31 |
|
flye
|
public |
A fast and accurate de novo assembler for single molecule sequencing reads using repeat graphs.
|
2024-08-30 |
|
fastahack
|
public |
No Summary
|
2024-08-30 |
|
evidencemodeler
|
public |
Evidence Modeler combines ab intio gene predictions, protein alignments, and transcript alignments into weighted consensus gene structures
|
2024-08-30 |
|
wisecondorx
|
public |
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
|
2024-08-29 |
|
trimal
|
public |
A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
|
2024-08-28 |
|
ucsc-fatotwobit
|
public |
Convert DNA from fasta to 2bit format
|
2024-08-28 |
|
ucsc-bigwigsummary
|
public |
Extract summary information from a bigWig file.
|
2024-08-28 |
|
meme
|
public |
Motif-based sequence analysis tools.
|
2024-08-28 |
|
ucsc-catdir
|
public |
concatenate files in directory to stdout.
|
2024-08-27 |
|
ucsc-hgloadoutjoined
|
public |
load new style (2014) RepeatMasker .out files into database
|
2024-08-27 |
|
ucsc-bedremoveoverlap
|
public |
Remove overlapping records from a (sorted) bed file. Gets rid of
|
2024-08-27 |
|
ucsc-maffetch
|
public |
get overlapping records from an MAF using an index table
|
2024-08-27 |
|
ucsc-gff3togenepred
|
public |
convert a GFF3 file to a genePred file
|
2024-08-27 |
