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Protocols

seq_crumbs specifications

Information


Unique identifier OMICS_01075
Name seq_crumbs
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • sff_extract

Versioning


No version available

seq_crumbs citations

 (14)
library_books

Resistance to Plum Pox Virus (PPV) in apricot (Prunus armeniaca L.) is associated with down regulation of two MATHd genes

2018
BMC Plant Biol
PMCID: 5787289
PMID: 29374454
DOI: 10.1186/s12870-018-1237-1

[…] (http://hannonlab.cshl.edu/fastx_toolkit) with a minimum quality score of 25 and a minimum length of 40. adaptor sequences were trimmed using the ‘trim_blast_short’ script available as part of seq_crumbs (http://bioinf.comav.upv.es/seq_crumbs/). high quality reads of all samples were combined in order to perform the de novo assembly using the trinity v.20140413p1 software [] (see […]

library_books

A transcribed enhancer dictates mesendoderm specification in pluripotency

2017
Nat Commun
PMCID: 5703900
PMID: 29180618
DOI: 10.1038/s41467-017-01804-w

[…] selection. libraries were sequenced with the illumina hiseq2000 (1 × 100 bp). purity-filtered reads were adapter and quality trimmed with cutadapt (v. 1.3), and filtered for low complexity with seq_crumbs (v. 0.1.8). reads were aligned against the mus musculus.grcm38.82 genome using star (v. 2.4.2a). the number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) using […]

library_books

Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background

2017
Front Plant Sci
PMCID: 5582342
PMID: 28912788
DOI: 10.3389/fpls.2017.01477

[…] that presented less coverage than 15, a mapping quality of 20 or a base quality of 20. in order to select the most reliable snps for genotyping the plants with hrm, different filters from the seq crumbs tools (https://bioinf.comav.upv.es/seq_crumbs/) were applied to the vcf file for maximizing the polymorphism validation. the filters cs60 and cl60 identified polymorphisms […]

library_books

De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei)

2017
PLoS One
PMCID: 5536302
PMID: 28759564
DOI: 10.1371/journal.pone.0179061

[…] leading:30 trailing:30 minlen:25. cleaned paired reads were concatenated across both samples to form combined left.fastq and right.fastq files. the calculate_stats utility from seq_crumbs was used to calculate q20 and q30 using the command calculate_stats–c [left.fastq,right.fastq] > out.txt []. cleaned paired reads were combined across both samples and passed to trinity […]

library_books

HDAC3 is a molecular brake of the metabolic switch supporting white adipose tissue browning

2017
Nat Commun
PMCID: 5522415
PMID: 28733645
DOI: 10.1038/s41467-017-00182-7

[…] reagents. sequencing data were processed using the illumina pipeline casava 1.82. purity-filtered reads were adapter and quality trimmed with cutadapt (v. 1.3, and filtered for low complexity with seq_crumbs (v. 0.1.8). reads were aligned against mus musculus (version grcm38) genome using star (v. 2.4.2a,. the number of read counts per gene locus was summarized with htseq-count (v. 0.6.1,) […]

library_books

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

2017
PLoS One
PMCID: 5392050
PMID: 28410402
DOI: 10.1371/journal.pone.0175091

[…] with fastqc software v 0.10.1 [] to inspect the length and quality of the reads. processing and trimming of the low-quality ends of the sequences were performed with the program trim_edges from the seq_crumbs-0.1.8 package based on the graphs generated with the fastqc software. eighteen nucleotides from 5’-ends (sequencing primer and mid sequences) and 22 nucleotides from 3’-ends (low-quality […]


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