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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
Proper citation: SAMTOOLS (RRID:SCR_002105) Copy
http://samtools.sourceforge.net/mpileup.shtml
Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Proper citation: SAMtools/BCFtools (RRID:SCR_005227) Copy
https://github.com/tseemann/shovill
Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.
Proper citation: shovill (RRID:SCR_017077) Copy
https://bitbucket.org/dranew/defuse
Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.
Proper citation: deFuse (RRID:SCR_003279) Copy
https://github.com/katholt/srst2
Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
Proper citation: Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) Copy
https://github.com/WangHYLab/fcirc
Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs.
Proper citation: Fcirc (RRID:SCR_018090) Copy
Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.
Proper citation: SNVer (RRID:SCR_002061) Copy
Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.
Proper citation: bio.tools (RRID:SCR_014695) Copy
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